ICGRC Omics API Demo (cannabinoid genes SNP clusters and Hemp/Drug label matching, datasource independent)¶
About this notebook *Cannabinoid genes SNPs are clustered and compared with legacy hemp/drug samples information, with data source (PRJN) independence test *
%matplotlib inline
%load_ext autoreload
import os
import requests
from IPython.display import display, Image, FileLink
#from jupyter_datatables import init_datatables_mode
#from ipydatagrid import DataGrid
from itables import init_notebook_mode
init_notebook_mode(all_interactive=True)
#init_notebook_mode(connected=True)
import itables.options as itablesopt
# display table options
#itablesopt.lengthMenu = [2, 5, 10, 20, 50, 100, 200, 500]
#itablesopt.maxBytes = 10000 , 0 to disable
#itablesopt.maxRows
#itablesopt.maxColumns
#%load_ext jupyter_require
#%requirejs d3 https://d3js.org/d3.v5.min
#init_datatables_mode()
%autoreload 2
import omics_api
from omics_api import *
REQUERY_URL=False
DEBUGGNG=False
myunit='percent_of_dw'
if DEBUGGNG:
setVariables(loglevel=getSetting('SHOW_DEBUG'),keep_unit=myunit)
else:
setVariables(loglevel=getSetting('SHOW_ERRORONLY'),keep_unit=myunit)
#setVariables(loglevel=getSetting('SHOW_ERRORONLY'))
"set variables: \nkeep_unit=percent_of_dw\nr_path=Rscript\nplink_path=plink\nLOG_LEVEL=1\nunit_converter={('percent_of_dw', 'ug_per_gdw'): 10000.0, ('ug_per_gdw', 'percent_of_dw'): 0.0001}"
Gene genes with cannabinoid annotations
urlgenes='https://icgrc.info/api/user/gene/cannabid,cannabic,cannabiv,cannabin?annot=cs10&accession=all'
labelgenes='cannab'
df_raw= read_url(urlgenes, labelgenes,requery=REQUERY_URL)
display(df_raw)
name | contig | fmin | fmax | strand | gb_keyword | go_term | interpro_value | |
---|---|---|---|---|---|---|---|---|
Loading... (need help?) |
Query each gene region, compare clustering based on SNPs and based on Hemp/Drug sample information. The steps are:
- Convert SNPs to plink and use plink --cluster ibs, with K=2
- Collect the samples for each cluster from SNPs
- Collect the samples for each hemp/drug from the cultivar_group property in sample
For each gene
- Calculate Variation of Information on the cluster and group partitions generated doi:10.1007/978-3-540-45167-9_14
- Calculate Jaccard index all cluster-pairs pairs
#setVariables(loglevel=getSetting('SHOW_DEBUG'))
DATADIR='data'
PLINKFILE=DATADIR + '/cs10-merge-wgs7ds-21trich-plink'
PLINKFILE=DATADIR + '/cs10-wgs7ds-genomicsdb-allsnps.isec_cds.snpeff.plink'
PLINKFILE=DATADIR + '/cs10-wgs7ds-genomicsdb-gatk4170.allsnpsonly-bcftools.filltags.fmis7maf05exchet9hwe9.plink'
PLINKFILE=DATADIR + '/cs10-wgs7ds-fmis5maf2exchet5hwe5qual100k' #600k
#draw_heatmap=['LOC115696986', 'LOC115697762']
vi_jaccard_scores=dict()
gene2range=dict()
projects=['PRJNA310948', 'PRJNA734114', 'PRJNA866500', 'PRJNA575581']
import itertools
drawtrees=['PRJNA310948-PRJNA734114-PRJNA866500-PRJNA575581'] #,'PRJNA310948-PRJNA575581','PRJNA734114-PRJNA575581']
projcombination= list(itertools.combinations(projects,4)) + list(itertools.combinations(projects,1)) + list(itertools.combinations(projects,2)) + list(itertools.combinations(projects,3))
for idx,row in df_raw.iterrows():
reg=row['contig'] + '_' + str(row['fmin']) + '_' + str(row['fmax'])
gene2range[row['name']]=(row['contig'],str(row['fmin']),str(row['fmax']),row['name'])
#print(reg + ' ' + row['name'] + ' ' + row['gb_keyword'])
urlloc='https://icgrc.info/api/user/variant/' + row['contig'] + ':' + str(row['fmin']) + '-' + str(row['fmax']) + '?snpds=7ds&ref=cs10'
df_snp= read_url(urlloc,reg,requery=REQUERY_URL)
#display(df_snp)
for prjcomb in projcombination:
prjcomb=list(prjcomb)
print(prjcomb)
df_hasgroup=df_snp.set_index('property',drop=False)
df_hasgroup=df_hasgroup.loc[:, df_hasgroup.loc['cultivar_group'].isin([TYPE_PROP,'cultivar_group','Hemp','Drug','BLDT','NLDT','Hemp-type','Drug-type','Drug type feral','Type I','Type III'])]
df_hasgroup=df_hasgroup.loc[:, df_hasgroup.loc['NCBI BioProject'].isin([TYPE_PROP,'NCBI BioProject'] + prjcomb)]
df_hasgroup=df_hasgroup.reset_index(drop=True)
#print('has group')
#display(df_hasgroup)
convert_group={'BLDT':'Drug','NLDT':'Drug','Hemp-type':'Hemp','Drug-type':'Drug','Drug type feral':'Drug','Type I':'Drug','Type III':'Hemp'}
heatmap=False #row['name'] in draw_heatmap
#if heatmap:
#vi_jaccard_scores['wgs7ds_600k']=do_phylo(df_hasgroup, 'cluster_' + reg,K=2,convert_group=convert_group,plink_file=PLINKFILE,plink_extract=[])
# group by project
comblabel="-".join(prjcomb)
drawtree= len(prjcomb)==1 or comblabel in drawtrees
pval=None
if len(prjcomb)>1:
vi_jaccard_scores['wgs7ds_600k_proj_' + comblabel]=do_phylo(df_hasgroup, 'cluster_byprjn_' + comblabel,K=2,cluster_group='NCBI BioProject',plink_file=PLINKFILE,recalc=True,drawtree=drawtree)
pval=vi_jaccard_scores['wgs7ds_600k_proj_' + comblabel][6]
if not drawtree and pval is not None and pval >0.05:
vi_jaccard_scores['wgs7ds_600k_proj_' + comblabel]=do_phylo(df_hasgroup, 'cluster_byprjn_' + comblabel,K=2,cluster_group='NCBI BioProject',plink_file=PLINKFILE,recalc=True,drawtree=True)
drawtree=drawtree or (pval is not None and pval >0.05)
vi_jaccard_scores['wgs7ds_600k_cult_' + comblabel]=do_phylo(df_hasgroup, 'cluster_bycult_' + comblabel,K=2,cluster_group='cultivar_group',convert_group=convert_group,plink_file=PLINKFILE,recalc=True,drawtree=drawtree)
break
listreg=[]
for reg in vi_jaccard_scores.keys():
print("\n" + reg)
j=vi_jaccard_scores[reg]
vi=None
nvi=None
J=None
if not j is None:
if j[0]:
#print("\nvi=" + str(j[0]))
#print("\njaccard=" + str(j[1]))
vi=j[0]
nvi=j[1]
J=str(j[2])
#j=(vi, mapGroupClust2Jaccard, mapGroup2Sample, mapCluster2Sample)
chistat=j[5]
chip=j[6]
listreg.append([reg,vi,nvi,chistat,chip,J])
import pandas as pd
pdviall=pd.DataFrame(listreg,columns=['region','VI','Normalized VI','chi2 statistics','chi2 pvalue','Jaccard'])
display(pdviall)
pdviall.to_csv('wgs7ds_600k_clusters_vi_all.tsv',sep="\t")
['PRJNA310948', 'PRJNA734114', 'PRJNA866500', 'PRJNA575581']
rm: cannot remove ‘cluster_byprjn_PRJNA310948-PRJNA734114-PRJNA866500-PRJNA575581*’: No such file or directory
group PRJNA310948 group PRJNA734114 group PRJNA866500 group PRJNA575581
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs Warning message: In for (i in seq_along(cenv$extra)) { : closing unused connection 3 (cluster_byprjn_PRJNA310948-PRJNA734114-PRJNA866500-PRJNA575581.bed)
'Variation of Information=0.9176026205214576 Normalized VI=0.48534659180689876'
'Chisquare statistics=None pvalue=None'
python draw-tree-3.py cluster_byprjn_PRJNA310948-PRJNA734114-PRJNA866500-PRJNA575581.newick
rm: cannot remove ‘cluster_bycult_PRJNA310948-PRJNA734114-PRJNA866500-PRJNA575581*’: No such file or directory
group Hemp group Drug
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs Warning message: In for (i in seq_along(cenv$extra)) { : closing unused connection 3 (cluster_bycult_PRJNA310948-PRJNA734114-PRJNA866500-PRJNA575581.bed)
'Variation of Information=1.5746361691069999 Normalized VI=0.8989416369601417'
chisquare_contingency xs=['Hemp', 'Drug'] ys=['1', '2'] [[58 81] [75 9]]
'chi2 statistic: 47.245'
'p-value: 6.2652e-12'
'degrees of freedom: 1'
'expected frequencies:'
array([[82.90134529, 56.09865471], [50.09865471, 33.90134529]])
'Chisquare statistics=47.24478678246089 pvalue=6.265239624400386e-12'
python draw-tree-3.py cluster_bycult_PRJNA310948-PRJNA734114-PRJNA866500-PRJNA575581.newick
['PRJNA310948'] group Hemp group Drug
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs Warning message: In for (uniq in uniqs[-1]) { : closing unused connection 3 (cluster_bycult_PRJNA310948.bed)
'Variation of Information=0.22897487687968646 Normalized VI=0.24351106629127672'
'Chisquare statistics=None pvalue=None'
python draw-tree-3.py cluster_bycult_PRJNA310948.newick
['PRJNA734114'] group Hemp group Drug
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs Warning message: In for (uniq in uniqs[-1]) { : closing unused connection 3 (cluster_bycult_PRJNA734114.bed)
'Variation of Information=0.0 Normalized VI=1.1102230246251565e-16'
'Chisquare statistics=None pvalue=None'
python draw-tree-3.py cluster_bycult_PRJNA734114.newick
['PRJNA866500'] group Hemp group Drug
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs Warning message: In for (i in seq_along(cenv$extra)) { : closing unused connection 3 (cluster_bycult_PRJNA866500.bed)
'Variation of Information=1.1803778630088229 Normalized VI=0.8969956226776346'
'Chisquare statistics=None pvalue=None'
python draw-tree-3.py cluster_bycult_PRJNA866500.newick
['PRJNA575581'] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs Warning message: In for (uniq in uniqs[-1]) { : closing unused connection 3 (cluster_bycult_PRJNA575581.bed)
'Variation of Information=1.0895439012021202 Normalized VI=0.7410178373915063'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[17 3] [ 1 8]]
'chi2 statistic: 11.426'
'p-value: 0.00072421'
'degrees of freedom: 1'
'expected frequencies:'
array([[12.4137931, 7.5862069], [ 5.5862069, 3.4137931]])
'Chisquare statistics=11.426073232323233 pvalue=0.0007242058061782072'
python draw-tree-3.py cluster_bycult_PRJNA575581.newick
['PRJNA310948', 'PRJNA734114'] group PRJNA310948 group PRJNA734114
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs Warning message: In for (i in seq_along(cenv$extra)) { : closing unused connection 3 (cluster_byprjn_PRJNA310948-PRJNA734114.bed)
'Variation of Information=1.7273024310089609 Normalized VI=0.9279014594282816'
chisquare_contingency xs=['PRJNA310948', 'PRJNA734114'] ys=['1', '2'] [[13 39] [35 17]]
'chi2 statistic: 17.062'
'p-value: 3.617e-05'
'degrees of freedom: 1'
'expected frequencies:'
array([[24., 28.], [24., 28.]])
'Chisquare statistics=17.0625 pvalue=3.616950510932097e-05'
rm: cannot remove ‘cluster_bycult_PRJNA310948-PRJNA734114*’: No such file or directory
group Hemp group Drug
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs Warning message: In for (i in seq_along(cenv$extra)) { : closing unused connection 3 (cluster_bycult_PRJNA310948-PRJNA734114.bed)
'Variation of Information=0.13730455498460814 Normalized VI=0.12888635927290393'
'Chisquare statistics=None pvalue=None'
['PRJNA310948', 'PRJNA866500'] group PRJNA310948 group PRJNA866500
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs Warning message: In for (i in seq_along(cenv$extra)) { : closing unused connection 3 (cluster_byprjn_PRJNA310948-PRJNA866500.bed)
'Variation of Information=0.0 Normalized VI=-4.440892098500626e-16'
'Chisquare statistics=None pvalue=None'
rm: cannot remove ‘cluster_bycult_PRJNA310948-PRJNA866500*’: No such file or directory
group Hemp group Drug
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs Warning message: In for (i in seq_along(cenv$extra)) { : closing unused connection 3 (cluster_bycult_PRJNA310948-PRJNA866500.bed)
'Variation of Information=1.2417522781739458 Normalized VI=0.7997399453941096'
chisquare_contingency xs=['Hemp', 'Drug'] ys=['1', '2'] [[81 14] [ 9 38]]
'chi2 statistic: 56.404'
'p-value: 5.9019e-14'
'degrees of freedom: 1'
'expected frequencies:'
array([[60.21126761, 34.78873239], [29.78873239, 17.21126761]])
'Chisquare statistics=56.40369359022215 pvalue=5.901939995660085e-14'
['PRJNA310948', 'PRJNA575581'] group PRJNA310948 group PRJNA575581
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs Warning message: In for (i in seq_along(cenv$extra)) { : closing unused connection 3 (cluster_byprjn_PRJNA310948-PRJNA575581.bed)
'Variation of Information=1.853859205290838 Normalized VI=0.9924507486753356'
chisquare_contingency xs=['PRJNA310948', 'PRJNA575581'] ys=['1', '2'] [[36 16] [16 13]]
'chi2 statistic: 1.0476'
'p-value: 0.30605'
'degrees of freedom: 1'
'expected frequencies:'
array([[33.38271605, 18.61728395], [18.61728395, 10.38271605]])
'Chisquare statistics=1.0476364121678197 pvalue=0.30605207100322007'
group PRJNA310948 group PRJNA575581
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs Warning message: In for (i in seq_along(cenv$extra)) { : closing unused connection 3 (cluster_byprjn_PRJNA310948-PRJNA575581.bed)
'Variation of Information=1.853859205290838 Normalized VI=0.9924507486753356'
chisquare_contingency xs=['PRJNA310948', 'PRJNA575581'] ys=['1', '2'] [[36 16] [16 13]]
'chi2 statistic: 1.0476'
'p-value: 0.30605'
'degrees of freedom: 1'
'expected frequencies:'
array([[33.38271605, 18.61728395], [18.61728395, 10.38271605]])
'Chisquare statistics=1.0476364121678197 pvalue=0.30605207100322007'
python draw-tree-3.py cluster_byprjn_PRJNA310948-PRJNA575581.newick
rm: cannot remove ‘cluster_bycult_PRJNA310948-PRJNA575581*’: No such file or directory
group Hemp group Drug
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs Warning message: In for (i in seq_along(cenv$extra)) { : closing unused connection 3 (cluster_bycult_PRJNA310948-PRJNA575581.bed)
'Variation of Information=0.8272073073926761 Normalized VI=0.6292902564534144'
chisquare_contingency xs=['Hemp', 'Drug'] ys=['1', '2'] [[ 1 22] [51 7]]
'chi2 statistic: 46.488'
'p-value: 9.2182e-12'
'degrees of freedom: 1'
'expected frequencies:'
array([[14.7654321, 8.2345679], [37.2345679, 20.7654321]])
'Chisquare statistics=46.4879812663297 pvalue=9.218212795056947e-12'
python draw-tree-3.py cluster_bycult_PRJNA310948-PRJNA575581.newick
['PRJNA734114', 'PRJNA866500'] group PRJNA734114 group PRJNA866500
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs Warning message: In for (i in seq_along(cenv$extra)) { : closing unused connection 3 (cluster_byprjn_PRJNA734114-PRJNA866500.bed)
'Variation of Information=0.0 Normalized VI=-4.440892098500626e-16'
'Chisquare statistics=None pvalue=None'
rm: cannot remove ‘cluster_bycult_PRJNA734114-PRJNA866500*’: No such file or directory
group Hemp group Drug
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs Warning message: In for (i in seq_along(cenv$extra)) { : closing unused connection 3 (cluster_bycult_PRJNA734114-PRJNA866500.bed)
'Variation of Information=1.52316178758834 Normalized VI=0.9647353286665041'
chisquare_contingency xs=['Hemp', 'Drug'] ys=['1', '2'] [[35 81] [17 9]]
'chi2 statistic: 9.88'
'p-value: 0.0016708'
'degrees of freedom: 1'
'expected frequencies:'
array([[42.47887324, 73.52112676], [ 9.52112676, 16.47887324]])
'Chisquare statistics=9.880034545104175 pvalue=0.0016708180210108095'
['PRJNA734114', 'PRJNA575581'] group PRJNA734114 group PRJNA575581
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs Warning message: In for (i in seq_along(cenv$extra)) { : closing unused connection 3 (cluster_byprjn_PRJNA734114-PRJNA575581.bed)
'Variation of Information=1.722889686663157 Normalized VI=0.9411687470523271'
chisquare_contingency xs=['PRJNA734114', 'PRJNA575581'] ys=['1', '2'] [[17 35] [21 8]]
'chi2 statistic: 10.254'
'p-value: 0.0013642'
'degrees of freedom: 1'
'expected frequencies:'
array([[24.39506173, 27.60493827], [13.60493827, 15.39506173]])
'Chisquare statistics=10.253637982169353 pvalue=0.001364153132874646'
rm: cannot remove ‘cluster_bycult_PRJNA734114-PRJNA575581*’: No such file or directory
group Hemp group Drug
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs Warning message: In for (i in seq_along(cenv$extra)) { : closing unused connection 3 (cluster_bycult_PRJNA734114-PRJNA575581.bed)
'Variation of Information=0.16737133025229584 Normalized VI=0.15502893818254748'
'Chisquare statistics=None pvalue=None'
['PRJNA866500', 'PRJNA575581'] group PRJNA866500 group PRJNA575581
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs Warning message: In for (i in seq_along(cenv$extra)) { : closing unused connection 3 (cluster_byprjn_PRJNA866500-PRJNA575581.bed)
'Variation of Information=0.0 Normalized VI=2.220446049250313e-16'
'Chisquare statistics=None pvalue=None'
rm: cannot remove ‘cluster_bycult_PRJNA866500-PRJNA575581*’: No such file or directory
group Hemp group Drug
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs Warning message: In for (i in seq_along(cenv$extra)) { : closing unused connection 3 (cluster_bycult_PRJNA866500-PRJNA575581.bed)
'Variation of Information=1.1449271490925519 Normalized VI=0.83352372452778'
chisquare_contingency xs=['Hemp', 'Drug'] ys=['1', '2'] [[ 9 81] [20 9]]
'chi2 statistic: 38.238'
'p-value: 6.2619e-10'
'degrees of freedom: 1'
'expected frequencies:'
array([[21.93277311, 68.06722689], [ 7.06722689, 21.93277311]])
'Chisquare statistics=38.23806311563248 pvalue=6.261896334611219e-10'
['PRJNA310948', 'PRJNA734114', 'PRJNA866500']
rm: cannot remove ‘cluster_byprjn_PRJNA310948-PRJNA734114-PRJNA866500*’: No such file or directory
group PRJNA310948 group PRJNA734114 group PRJNA866500
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs Warning message: In for (i in seq_along(cenv$extra)) { : closing unused connection 3 (cluster_byprjn_PRJNA310948-PRJNA734114-PRJNA866500.bed)
'Variation of Information=0.5360824742268041 Normalized VI=0.34984961946291315'
'Chisquare statistics=None pvalue=None'
rm: cannot remove ‘cluster_bycult_PRJNA310948-PRJNA734114-PRJNA866500*’: No such file or directory
group Hemp group Drug
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs Warning message: In for (i in seq_along(cenv$extra)) { : closing unused connection 3 (cluster_bycult_PRJNA310948-PRJNA734114-PRJNA866500.bed)
'Variation of Information=1.5861589760091215 Normalized VI=0.9070970264604584'
chisquare_contingency xs=['Hemp', 'Drug'] ys=['1', '2'] [[49 81] [55 9]]
'chi2 statistic: 38.222'
'p-value: 6.3147e-10'
'degrees of freedom: 1'
'expected frequencies:'
array([[69.69072165, 60.30927835], [34.30927835, 29.69072165]])
'Chisquare statistics=38.22167347242768 pvalue=6.314712762264176e-10'
['PRJNA310948', 'PRJNA734114', 'PRJNA575581']
rm: cannot remove ‘cluster_byprjn_PRJNA310948-PRJNA734114-PRJNA575581*’: No such file or directory
group PRJNA310948 group PRJNA734114 group PRJNA575581
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs Warning message: In for (i in seq_along(cenv$extra)) { : closing unused connection 3 (cluster_byprjn_PRJNA310948-PRJNA734114-PRJNA575581.bed)
'Variation of Information=2.2744957407956057 Normalized VI=0.9487000744822588'
chisquare_contingency xs=['PRJNA310948', 'PRJNA734114', 'PRJNA575581'] ys=['1', '2'] [[39 13] [17 35] [21 8]]
'chi2 statistic: 22.298'
'p-value: 1.4386e-05'
'degrees of freedom: 2'
'expected frequencies:'
array([[30.10526316, 21.89473684], [30.10526316, 21.89473684], [16.78947368, 12.21052632]])
'Chisquare statistics=22.298483843742464 pvalue=1.4386188812423403e-05'
rm: cannot remove ‘cluster_bycult_PRJNA310948-PRJNA734114-PRJNA575581*’: No such file or directory
group Hemp group Drug
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs Warning message: In for (i in seq_along(cenv$extra)) { : closing unused connection 3 (cluster_bycult_PRJNA310948-PRJNA734114-PRJNA575581.bed)
'Variation of Information=0.19497882652999768 Normalized VI=0.1801105183878402'
'Chisquare statistics=None pvalue=None'
['PRJNA310948', 'PRJNA866500', 'PRJNA575581']
rm: cannot remove ‘cluster_byprjn_PRJNA310948-PRJNA866500-PRJNA575581*’: No such file or directory
group PRJNA310948 group PRJNA866500 group PRJNA575581
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs Warning message: In for (i in seq_along(cenv$extra)) { : closing unused connection 3 (cluster_byprjn_PRJNA310948-PRJNA866500-PRJNA575581.bed)
'Variation of Information=0.7198942990348454 Normalized VI=0.45510763081925265'
'Chisquare statistics=None pvalue=None'
rm: cannot remove ‘cluster_bycult_PRJNA310948-PRJNA866500-PRJNA575581*’: No such file or directory
group Hemp group Drug
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs Warning message: In for (i in seq_along(cenv$extra)) { : closing unused connection 3 (cluster_bycult_PRJNA310948-PRJNA866500-PRJNA575581.bed)
'Variation of Information=1.4169427314551304 Normalized VI=0.8377144650267704'
chisquare_contingency xs=['Hemp', 'Drug'] ys=['1', '2'] [[27 77] [58 9]]
'chi2 statistic: 57.471'
'p-value: 3.4305e-14'
'degrees of freedom: 1'
'expected frequencies:'
array([[51.69590643, 52.30409357], [33.30409357, 33.69590643]])
'Chisquare statistics=57.47071562534846 pvalue=3.43049012564994e-14'
['PRJNA734114', 'PRJNA866500', 'PRJNA575581']
rm: cannot remove ‘cluster_byprjn_PRJNA734114-PRJNA866500-PRJNA575581*’: No such file or directory
group PRJNA734114 group PRJNA866500 group PRJNA575581
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs Warning message: In for (i in seq_along(cenv$extra)) { : closing unused connection 3 (cluster_byprjn_PRJNA734114-PRJNA866500-PRJNA575581.bed)
'Variation of Information=0.44575167269952176 Normalized VI=0.3087452006027651'
'Chisquare statistics=None pvalue=None'
rm: cannot remove ‘cluster_bycult_PRJNA734114-PRJNA866500-PRJNA575581*’: No such file or directory
group Hemp group Drug
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs Warning message: In for (i in seq_along(cenv$extra)) { : closing unused connection 3 (cluster_bycult_PRJNA734114-PRJNA866500-PRJNA575581.bed)
'Variation of Information=1.5939042834784418 Normalized VI=0.9288649869138937'
chisquare_contingency xs=['Hemp', 'Drug'] ys=['1', '2'] [[44 81] [37 9]]
'chi2 statistic: 25.814'
'p-value: 3.7602e-07'
'degrees of freedom: 1'
'expected frequencies:'
array([[59.21052632, 65.78947368], [21.78947368, 24.21052632]])
'Chisquare statistics=25.813647826086957 pvalue=3.7602022027776207e-07'
wgs7ds_600k_proj_PRJNA310948-PRJNA734114-PRJNA866500-PRJNA575581 wgs7ds_600k_cult_PRJNA310948-PRJNA734114-PRJNA866500-PRJNA575581 wgs7ds_600k_cult_PRJNA310948 wgs7ds_600k_cult_PRJNA734114 wgs7ds_600k_cult_PRJNA866500 wgs7ds_600k_cult_PRJNA575581 wgs7ds_600k_proj_PRJNA310948-PRJNA734114 wgs7ds_600k_cult_PRJNA310948-PRJNA734114 wgs7ds_600k_proj_PRJNA310948-PRJNA866500 wgs7ds_600k_cult_PRJNA310948-PRJNA866500 wgs7ds_600k_proj_PRJNA310948-PRJNA575581 wgs7ds_600k_cult_PRJNA310948-PRJNA575581 wgs7ds_600k_proj_PRJNA734114-PRJNA866500 wgs7ds_600k_cult_PRJNA734114-PRJNA866500 wgs7ds_600k_proj_PRJNA734114-PRJNA575581 wgs7ds_600k_cult_PRJNA734114-PRJNA575581 wgs7ds_600k_proj_PRJNA866500-PRJNA575581 wgs7ds_600k_cult_PRJNA866500-PRJNA575581 wgs7ds_600k_proj_PRJNA310948-PRJNA734114-PRJNA866500 wgs7ds_600k_cult_PRJNA310948-PRJNA734114-PRJNA866500 wgs7ds_600k_proj_PRJNA310948-PRJNA734114-PRJNA575581 wgs7ds_600k_cult_PRJNA310948-PRJNA734114-PRJNA575581 wgs7ds_600k_proj_PRJNA310948-PRJNA866500-PRJNA575581 wgs7ds_600k_cult_PRJNA310948-PRJNA866500-PRJNA575581 wgs7ds_600k_proj_PRJNA734114-PRJNA866500-PRJNA575581 wgs7ds_600k_cult_PRJNA734114-PRJNA866500-PRJNA575581
region | VI | Normalized VI | chi2 statistics | chi2 pvalue | Jaccard |
---|---|---|---|---|---|
Loading... (need help?) |
#pdvi_all_byproj=pd.concat([pdvi1,pdvi2, pdvi3])
#display(pdvi_all_byproj)
Repeat for the best (lowest VI) and worst (largest VI)) cluster match, showing heatmap and clusters, and using the API module do_clustering
show_clusters=['LOC115697762','LOC115696986']
prjcomb=['PRJNA310948','PRJNA575581']
convert_group={'BLDT':'Drug','NLDT':'Drug','Hemp-type':'Hemp','Drug-type':'Drug','Drug type feral':'Drug','Type I':'Drug','Type III':'Hemp'}
gene2range=dict()
for idx,row in df_raw.iterrows():
gene2range[row['name']]=(row['contig'],str(row['fmin']),str(row['fmax']),row['name'])
if row['name'] in show_clusters:
reg=row['contig'] + '_' + str(row['fmin']) + '_' + str(row['fmax'])
gene2rangei=[(row['contig'],str(row['fmin']),str(row['fmax']),row['name'])]
print(reg + ' ' + row['name'] + ' ' + row['gb_keyword'])
urlloc='https://icgrc.info/api/user/variant/' + row['contig'] + ':' + str(row['fmin']) + '-' + str(row['fmax']) + '?snpds=7ds&ref=cs10'
df_snp= read_url(urlloc,reg,requery=REQUERY_URL)
display(df_snp)
df_snp_prjn=df_snp.set_index('property',drop=False)
df_snp_prjn=df_snp_prjn.loc[:, df_snp_prjn.loc['NCBI BioProject'].isin([TYPE_PROP,'NCBI BioProject'] + prjcomb)]
df_snp_prjn=df_snp_prjn.reset_index(drop=True)
display(df_snp_prjn)
do_clustering(df_snp_prjn,row['name'],'cultivar_group',convert_group=convert_group,K=2,heatmap=False,plink_file=PLINKFILE)
break
NC_044378.1_30980884_30982768 LOC115697762 cannabidiolic acid synthase
datatype | property | SAMN00738286 | SAMN04480086 | SAMN04480087 | SAMN04480088 | SAMN04480089 | SAMN04480090 | SAMN04480091 | SAMN04480092 | SAMN04480093 | SAMN04480094 | SAMN04480095 | SAMN04480097 | SAMN04480101 | SAMN04480102 | SAMN04480103 | SAMN04480106 | SAMN04480109 | SAMN04480113 | SAMN04480122 | SAMN04480132 | SAMN04480139 | SAMN04480148 | SAMN04480154 | SAMN04480156 | SAMN04480157 | SAMN04480159 | SAMN04480165 | SAMN04480167 | SAMN04480168 | SAMN04480171 | SAMN04480192 | SAMN04480193 | SAMN04480194 | SAMN04480195 | SAMN04480196 | SAMN04480197 | SAMN04480202 | SAMN04480206 | SAMN04480207 | SAMN04480212 | SAMN04480216 | SAMN04480217 | SAMN04480219 | SAMN30166951 | SAMN30166952 | SAMN30166953 | SAMN30166954 | SAMN30166955 | SRR10578250 | SRR10578251 | SRR10578252 | SRR10578253 | SRR10578254 | SRR10578255 | SRR10578256 | SRR10578257 | SRR10578258 | SRR10578259 | SRR10578260 | SRR10578261 | SRR10578262 | SRR10578263 | SRR10578264 | SRR10578265 | SRR10578266 | SRR10578267 | SRR10578268 | SRR10578269 | SRR10578270 | SRR10578271 | SRR10578272 | SRR10578273 | SRR10578274 | SRR10578275 | SRR10578276 | SRR10578277 | SRR10578278 | SRR10578279 | SRR10578280 | SRR10578281 | SRR10578282 | SRR10578283 | SRR10578284 | SRR10578285 | SRR10578286 | SRR10578287 | SRR10578288 | SRR10578289 | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Loading... (need help?) |
datatype | property | SAMN04480086 | SAMN04480087 | SAMN04480088 | SAMN04480089 | SAMN04480090 | SAMN04480091 | SAMN04480092 | SAMN04480093 | SAMN04480094 | SAMN04480095 | SAMN04480097 | SAMN04480101 | SAMN04480102 | SAMN04480103 | SAMN04480106 | SAMN04480109 | SAMN04480113 | SAMN04480122 | SAMN04480132 | SAMN04480139 | SAMN04480148 | SAMN04480154 | SAMN04480156 | SAMN04480157 | SAMN04480159 | SAMN04480165 | SAMN04480167 | SAMN04480168 | SAMN04480171 | SAMN04480192 | SAMN04480193 | SAMN04480194 | SAMN04480195 | SAMN04480196 | SAMN04480197 | SAMN04480202 | SAMN04480206 | SAMN04480207 | SAMN04480212 | SAMN04480216 | SAMN04480217 | SAMN04480219 | SAMN04480233 | SAMN04480248 | SAMN04480249 | SAMN04480250 | SAMN04480253 | SAMN04480272 | SRR10578250 | SRR10578251 | SRR10578252 | SRR10578253 | SRR10578254 | SRR10578255 | SRR10578256 | SRR10578257 | SRR10578258 | SRR10578259 | SRR10578260 | SRR10578261 | SRR10578262 | SRR10578263 | SRR10578264 | SRR10578265 | SRR10578266 | SRR10578267 | SRR10578268 | SRR10578269 | SRR10578270 | SRR10578271 | SRR10578272 | SRR10578273 | SRR10578274 | SRR10578275 | SRR10578276 | SRR10578277 | SRR10578278 | SRR10578279 | SRR10578280 | SRR10578281 | SRR10578282 | SRR10578283 | SRR10578284 | SRR10578285 | SRR10578286 | SRR10578287 | SRR10578288 | SRR10578289 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Loading... (need help?) |
group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
Extend by using mutiple G genes combinations
for idx,row in df_raw.iterrows():
reg=row['contig'] + '_' + str(row['fmin']) + '_' + str(row['fmax'])
gene2range[row['name']]=(row['contig'],str(row['fmin']),str(row['fmax']),row['name'])
import itertools
G=1
#genecombination=list(itertools.combinations(df_raw['name'].tolist(),G))
genecombination=list(itertools.combinations(df_raw['name'].tolist(),1)) + list(itertools.combinations(df_raw['name'].tolist(),2)) + list(itertools.combinations(df_raw['name'].tolist(),3))
display(genecombination)
[('LOC115717841',), ('LOC115718836',), ('LOC115720716',), ('LOC115697880',), ('LOC115696909',), ('LOC115696884',), ('LOC115697762',), ('LOC115696987',), ('LOC115696986',), ('LOC115697126',), ('LOC115697019',), ('LOC115717841', 'LOC115718836'), ('LOC115717841', 'LOC115720716'), ('LOC115717841', 'LOC115697880'), ('LOC115717841', 'LOC115696909'), ('LOC115717841', 'LOC115696884'), ('LOC115717841', 'LOC115697762'), ('LOC115717841', 'LOC115696987'), ('LOC115717841', 'LOC115696986'), ('LOC115717841', 'LOC115697126'), ('LOC115717841', 'LOC115697019'), ('LOC115718836', 'LOC115720716'), ('LOC115718836', 'LOC115697880'), ('LOC115718836', 'LOC115696909'), ('LOC115718836', 'LOC115696884'), ('LOC115718836', 'LOC115697762'), ('LOC115718836', 'LOC115696987'), ('LOC115718836', 'LOC115696986'), ('LOC115718836', 'LOC115697126'), ('LOC115718836', 'LOC115697019'), ('LOC115720716', 'LOC115697880'), ('LOC115720716', 'LOC115696909'), ('LOC115720716', 'LOC115696884'), ('LOC115720716', 'LOC115697762'), ('LOC115720716', 'LOC115696987'), ('LOC115720716', 'LOC115696986'), ('LOC115720716', 'LOC115697126'), ('LOC115720716', 'LOC115697019'), ('LOC115697880', 'LOC115696909'), ('LOC115697880', 'LOC115696884'), ('LOC115697880', 'LOC115697762'), ('LOC115697880', 'LOC115696987'), ('LOC115697880', 'LOC115696986'), ('LOC115697880', 'LOC115697126'), ('LOC115697880', 'LOC115697019'), ('LOC115696909', 'LOC115696884'), ('LOC115696909', 'LOC115697762'), ('LOC115696909', 'LOC115696987'), ('LOC115696909', 'LOC115696986'), ('LOC115696909', 'LOC115697126'), ('LOC115696909', 'LOC115697019'), ('LOC115696884', 'LOC115697762'), ('LOC115696884', 'LOC115696987'), ('LOC115696884', 'LOC115696986'), ('LOC115696884', 'LOC115697126'), ('LOC115696884', 'LOC115697019'), ('LOC115697762', 'LOC115696987'), ('LOC115697762', 'LOC115696986'), ('LOC115697762', 'LOC115697126'), ('LOC115697762', 'LOC115697019'), ('LOC115696987', 'LOC115696986'), ('LOC115696987', 'LOC115697126'), ('LOC115696987', 'LOC115697019'), ('LOC115696986', 'LOC115697126'), ('LOC115696986', 'LOC115697019'), ('LOC115697126', 'LOC115697019'), ('LOC115717841', 'LOC115718836', 'LOC115720716'), ('LOC115717841', 'LOC115718836', 'LOC115697880'), ('LOC115717841', 'LOC115718836', 'LOC115696909'), ('LOC115717841', 'LOC115718836', 'LOC115696884'), ('LOC115717841', 'LOC115718836', 'LOC115697762'), ('LOC115717841', 'LOC115718836', 'LOC115696987'), ('LOC115717841', 'LOC115718836', 'LOC115696986'), ('LOC115717841', 'LOC115718836', 'LOC115697126'), ('LOC115717841', 'LOC115718836', 'LOC115697019'), ('LOC115717841', 'LOC115720716', 'LOC115697880'), ('LOC115717841', 'LOC115720716', 'LOC115696909'), ('LOC115717841', 'LOC115720716', 'LOC115696884'), ('LOC115717841', 'LOC115720716', 'LOC115697762'), ('LOC115717841', 'LOC115720716', 'LOC115696987'), ('LOC115717841', 'LOC115720716', 'LOC115696986'), ('LOC115717841', 'LOC115720716', 'LOC115697126'), ('LOC115717841', 'LOC115720716', 'LOC115697019'), ('LOC115717841', 'LOC115697880', 'LOC115696909'), ('LOC115717841', 'LOC115697880', 'LOC115696884'), ('LOC115717841', 'LOC115697880', 'LOC115697762'), ('LOC115717841', 'LOC115697880', 'LOC115696987'), ('LOC115717841', 'LOC115697880', 'LOC115696986'), ('LOC115717841', 'LOC115697880', 'LOC115697126'), ('LOC115717841', 'LOC115697880', 'LOC115697019'), ('LOC115717841', 'LOC115696909', 'LOC115696884'), ('LOC115717841', 'LOC115696909', 'LOC115697762'), ('LOC115717841', 'LOC115696909', 'LOC115696987'), ('LOC115717841', 'LOC115696909', 'LOC115696986'), ('LOC115717841', 'LOC115696909', 'LOC115697126'), ('LOC115717841', 'LOC115696909', 'LOC115697019'), ('LOC115717841', 'LOC115696884', 'LOC115697762'), ('LOC115717841', 'LOC115696884', 'LOC115696987'), ('LOC115717841', 'LOC115696884', 'LOC115696986'), ('LOC115717841', 'LOC115696884', 'LOC115697126'), ('LOC115717841', 'LOC115696884', 'LOC115697019'), ('LOC115717841', 'LOC115697762', 'LOC115696987'), ('LOC115717841', 'LOC115697762', 'LOC115696986'), ('LOC115717841', 'LOC115697762', 'LOC115697126'), ('LOC115717841', 'LOC115697762', 'LOC115697019'), ('LOC115717841', 'LOC115696987', 'LOC115696986'), ('LOC115717841', 'LOC115696987', 'LOC115697126'), ('LOC115717841', 'LOC115696987', 'LOC115697019'), ('LOC115717841', 'LOC115696986', 'LOC115697126'), ('LOC115717841', 'LOC115696986', 'LOC115697019'), ('LOC115717841', 'LOC115697126', 'LOC115697019'), ('LOC115718836', 'LOC115720716', 'LOC115697880'), ('LOC115718836', 'LOC115720716', 'LOC115696909'), ('LOC115718836', 'LOC115720716', 'LOC115696884'), ('LOC115718836', 'LOC115720716', 'LOC115697762'), ('LOC115718836', 'LOC115720716', 'LOC115696987'), ('LOC115718836', 'LOC115720716', 'LOC115696986'), ('LOC115718836', 'LOC115720716', 'LOC115697126'), ('LOC115718836', 'LOC115720716', 'LOC115697019'), ('LOC115718836', 'LOC115697880', 'LOC115696909'), ('LOC115718836', 'LOC115697880', 'LOC115696884'), ('LOC115718836', 'LOC115697880', 'LOC115697762'), ('LOC115718836', 'LOC115697880', 'LOC115696987'), ('LOC115718836', 'LOC115697880', 'LOC115696986'), ('LOC115718836', 'LOC115697880', 'LOC115697126'), ('LOC115718836', 'LOC115697880', 'LOC115697019'), ('LOC115718836', 'LOC115696909', 'LOC115696884'), ('LOC115718836', 'LOC115696909', 'LOC115697762'), ('LOC115718836', 'LOC115696909', 'LOC115696987'), ('LOC115718836', 'LOC115696909', 'LOC115696986'), ('LOC115718836', 'LOC115696909', 'LOC115697126'), ('LOC115718836', 'LOC115696909', 'LOC115697019'), ('LOC115718836', 'LOC115696884', 'LOC115697762'), ('LOC115718836', 'LOC115696884', 'LOC115696987'), ('LOC115718836', 'LOC115696884', 'LOC115696986'), ('LOC115718836', 'LOC115696884', 'LOC115697126'), ('LOC115718836', 'LOC115696884', 'LOC115697019'), ('LOC115718836', 'LOC115697762', 'LOC115696987'), ('LOC115718836', 'LOC115697762', 'LOC115696986'), ('LOC115718836', 'LOC115697762', 'LOC115697126'), ('LOC115718836', 'LOC115697762', 'LOC115697019'), ('LOC115718836', 'LOC115696987', 'LOC115696986'), ('LOC115718836', 'LOC115696987', 'LOC115697126'), ('LOC115718836', 'LOC115696987', 'LOC115697019'), ('LOC115718836', 'LOC115696986', 'LOC115697126'), ('LOC115718836', 'LOC115696986', 'LOC115697019'), ('LOC115718836', 'LOC115697126', 'LOC115697019'), ('LOC115720716', 'LOC115697880', 'LOC115696909'), ('LOC115720716', 'LOC115697880', 'LOC115696884'), ('LOC115720716', 'LOC115697880', 'LOC115697762'), ('LOC115720716', 'LOC115697880', 'LOC115696987'), ('LOC115720716', 'LOC115697880', 'LOC115696986'), ('LOC115720716', 'LOC115697880', 'LOC115697126'), ('LOC115720716', 'LOC115697880', 'LOC115697019'), ('LOC115720716', 'LOC115696909', 'LOC115696884'), ('LOC115720716', 'LOC115696909', 'LOC115697762'), ('LOC115720716', 'LOC115696909', 'LOC115696987'), ('LOC115720716', 'LOC115696909', 'LOC115696986'), ('LOC115720716', 'LOC115696909', 'LOC115697126'), ('LOC115720716', 'LOC115696909', 'LOC115697019'), ('LOC115720716', 'LOC115696884', 'LOC115697762'), ('LOC115720716', 'LOC115696884', 'LOC115696987'), ('LOC115720716', 'LOC115696884', 'LOC115696986'), ('LOC115720716', 'LOC115696884', 'LOC115697126'), ('LOC115720716', 'LOC115696884', 'LOC115697019'), ('LOC115720716', 'LOC115697762', 'LOC115696987'), ('LOC115720716', 'LOC115697762', 'LOC115696986'), ('LOC115720716', 'LOC115697762', 'LOC115697126'), ('LOC115720716', 'LOC115697762', 'LOC115697019'), ('LOC115720716', 'LOC115696987', 'LOC115696986'), ('LOC115720716', 'LOC115696987', 'LOC115697126'), ('LOC115720716', 'LOC115696987', 'LOC115697019'), ('LOC115720716', 'LOC115696986', 'LOC115697126'), ('LOC115720716', 'LOC115696986', 'LOC115697019'), ('LOC115720716', 'LOC115697126', 'LOC115697019'), ('LOC115697880', 'LOC115696909', 'LOC115696884'), ('LOC115697880', 'LOC115696909', 'LOC115697762'), ('LOC115697880', 'LOC115696909', 'LOC115696987'), ('LOC115697880', 'LOC115696909', 'LOC115696986'), ('LOC115697880', 'LOC115696909', 'LOC115697126'), ('LOC115697880', 'LOC115696909', 'LOC115697019'), ('LOC115697880', 'LOC115696884', 'LOC115697762'), ('LOC115697880', 'LOC115696884', 'LOC115696987'), ('LOC115697880', 'LOC115696884', 'LOC115696986'), ('LOC115697880', 'LOC115696884', 'LOC115697126'), ('LOC115697880', 'LOC115696884', 'LOC115697019'), ('LOC115697880', 'LOC115697762', 'LOC115696987'), ('LOC115697880', 'LOC115697762', 'LOC115696986'), ('LOC115697880', 'LOC115697762', 'LOC115697126'), ('LOC115697880', 'LOC115697762', 'LOC115697019'), ('LOC115697880', 'LOC115696987', 'LOC115696986'), ('LOC115697880', 'LOC115696987', 'LOC115697126'), ('LOC115697880', 'LOC115696987', 'LOC115697019'), ('LOC115697880', 'LOC115696986', 'LOC115697126'), ('LOC115697880', 'LOC115696986', 'LOC115697019'), ('LOC115697880', 'LOC115697126', 'LOC115697019'), ('LOC115696909', 'LOC115696884', 'LOC115697762'), ('LOC115696909', 'LOC115696884', 'LOC115696987'), ('LOC115696909', 'LOC115696884', 'LOC115696986'), ('LOC115696909', 'LOC115696884', 'LOC115697126'), ('LOC115696909', 'LOC115696884', 'LOC115697019'), ('LOC115696909', 'LOC115697762', 'LOC115696987'), ('LOC115696909', 'LOC115697762', 'LOC115696986'), ('LOC115696909', 'LOC115697762', 'LOC115697126'), ('LOC115696909', 'LOC115697762', 'LOC115697019'), ('LOC115696909', 'LOC115696987', 'LOC115696986'), ('LOC115696909', 'LOC115696987', 'LOC115697126'), ('LOC115696909', 'LOC115696987', 'LOC115697019'), ('LOC115696909', 'LOC115696986', 'LOC115697126'), ('LOC115696909', 'LOC115696986', 'LOC115697019'), ('LOC115696909', 'LOC115697126', 'LOC115697019'), ('LOC115696884', 'LOC115697762', 'LOC115696987'), ('LOC115696884', 'LOC115697762', 'LOC115696986'), ('LOC115696884', 'LOC115697762', 'LOC115697126'), ('LOC115696884', 'LOC115697762', 'LOC115697019'), ('LOC115696884', 'LOC115696987', 'LOC115696986'), ('LOC115696884', 'LOC115696987', 'LOC115697126'), ('LOC115696884', 'LOC115696987', 'LOC115697019'), ('LOC115696884', 'LOC115696986', 'LOC115697126'), ('LOC115696884', 'LOC115696986', 'LOC115697019'), ('LOC115696884', 'LOC115697126', 'LOC115697019'), ('LOC115697762', 'LOC115696987', 'LOC115696986'), ('LOC115697762', 'LOC115696987', 'LOC115697126'), ('LOC115697762', 'LOC115696987', 'LOC115697019'), ('LOC115697762', 'LOC115696986', 'LOC115697126'), ('LOC115697762', 'LOC115696986', 'LOC115697019'), ('LOC115697762', 'LOC115697126', 'LOC115697019'), ('LOC115696987', 'LOC115696986', 'LOC115697126'), ('LOC115696987', 'LOC115696986', 'LOC115697019'), ('LOC115696987', 'LOC115697126', 'LOC115697019'), ('LOC115696986', 'LOC115697126', 'LOC115697019')]
vi_jaccard_scores=dict()
#draw_heatmap=['LOC115720716_LOC115696884_LOC115697126','LOC115696884_LOC115697126_LOC115697019','LOC115718836_LOC115697762_LOC115696987']
#draw_heatmap=['LOC115696909_LOC115696987_LOC115696986','LOC115718836_LOC115696987_LOC115696986']
for row in genecombination:
# query for properties, use one gene
gene1=row[0]
gene1range=gene2range[gene1]
urlloc='https://icgrc.info/api/user/variant/' + gene1range[0] + ':' + gene1range[1] + '-' + gene1range[2] + '?snpds=7ds&ref=cs10'
reg=gene1range[0] + '_' + gene1range[1] + '_' + gene1range[2]
df_snp= read_url(urlloc,reg,requery=REQUERY_URL)
df_snp_prjn=df_snp.set_index('property',drop=False)
df_snp_prjn=df_snp_prjn.loc[:, df_snp_prjn.loc['NCBI BioProject'].isin([TYPE_PROP,'NCBI BioProject'] + prjcomb)]
df_snp_prjn=df_snp_prjn.reset_index(drop=True)
#display(df_snp_prjn)
reg="_".join(row)
plink_extract=[]
for combs in list(row):
plink_extract.append(gene2range[combs])
print(plink_extract)
vi_jaccard_scores[reg]=do_clustering(df_snp_prjn,reg,'cultivar_group',convert_group=convert_group,K=2,heatmap=False,plink_file=PLINKFILE,plink_extract=plink_extract)
listreg=[]
for reg in vi_jaccard_scores.keys():
print("\n" + reg)
j=vi_jaccard_scores[reg]
vi=None
nvi=None
J=None
if not j is None:
if j[0]:
vi=j[0]
nvi=j[1]
J=str(j[2])
chistat=j[5]
chip=j[6]
listreg.append([reg,vi,nvi,chistat,chip,J])
pdvi2=pd.DataFrame(listreg,columns=['region','VI','Normalized VI','chi2 statistics','chi2 pvalue','Jaccard'])
display(pdvi2)
pdvi2.to_csv(labelgenes + '_clusters_vi_prjn_' + str(G) +'.tsv',sep="\t")
[('NC_044374.1', '52617968', '52619389', 'LOC115717841')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.290316631308452 Normalized VI=0.9697874454976867'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[18 40] [ 6 3]]
'chi2 statistic: 2.8924'
'p-value: 0.088996'
'degrees of freedom: 1'
'expected frequencies:'
array([[20.7761194, 37.2238806], [ 3.2238806, 5.7761194]])
'Chisquare statistics=2.89243954008138 pvalue=0.0889960735982675'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.300498125927381 Normalized VI=0.9468273786191055'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[40 18] [ 2 7]]
'chi2 statistic: 5.4165'
'p-value: 0.019947'
'degrees of freedom: 1'
'expected frequencies:'
array([[36.35820896, 21.64179104], [ 5.64179104, 3.35820896]])
'Chisquare statistics=5.416505655902208 pvalue=0.01994724291925309'
[('NC_044375.1', '15324213', '15325849', 'LOC115720716')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.43910109638552 Normalized VI=0.979847413754684'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[28 30] [ 7 2]]
'chi2 statistic: 1.664'
'p-value: 0.19706'
'degrees of freedom: 1'
'expected frequencies:'
array([[30.29850746, 27.70149254], [ 4.70149254, 4.29850746]])
'Chisquare statistics=1.6640270080733446 pvalue=0.19706048130311465'
[('NC_044378.1', '25821934', '25823723', 'LOC115697880')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.2566276011135336 Normalized VI=0.9302187453623346'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '25916956', '25917584', 'LOC115696909')] group Drug group Hemp
Error: All variants excluded by '--extract range'.
'No variant for cluster_LOC115696909'
'Variation of Information=0.0 Normalized VI=None'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '29635083', '29636878', 'LOC115696884')] group Drug group Hemp
Error: All variants excluded by '--extract range'.
'No variant for cluster_LOC115696884'
'Variation of Information=0.0 Normalized VI=None'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '30980884', '30982768', 'LOC115697762')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '34047624', '34048440', 'LOC115696987')] group Drug group Hemp
Error: All variants excluded by '--extract range'.
'No variant for cluster_LOC115696987'
'Variation of Information=0.0 Normalized VI=None'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '34056091', '34061726', 'LOC115696986')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.1157168153563997 Normalized VI=0.9194356121210085'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.2519233055291332 Normalized VI=0.9366598417603532'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.9695982766150801 Normalized VI=0.9560189026592211'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[51 7] [ 5 4]]
'chi2 statistic: 3.8256'
'p-value: 0.050475'
'degrees of freedom: 1'
'expected frequencies:'
array([[48.47761194, 9.52238806], [ 7.52238806, 1.47761194]])
'Chisquare statistics=3.8256230718515205 pvalue=0.05047457814685534'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044375.1', '15287394', '15289081', 'LOC115718836')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.221018420954975 Normalized VI=0.9619916910323038'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[16 42] [ 6 3]]
'chi2 statistic: 3.7689'
'p-value: 0.052213'
'degrees of freedom: 1'
'expected frequencies:'
array([[19.04477612, 38.95522388], [ 2.95522388, 6.04477612]])
'Chisquare statistics=3.768928267347807 pvalue=0.052213077586652085'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044375.1', '15324213', '15325849', 'LOC115720716')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.2131033231060533 Normalized VI=0.9619916910323038'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[16 42] [ 6 3]]
'chi2 statistic: 3.7689'
'p-value: 0.052213'
'degrees of freedom: 1'
'expected frequencies:'
array([[19.04477612, 38.95522388], [ 2.95522388, 6.04477612]])
'Chisquare statistics=3.768928267347807 pvalue=0.052213077586652085'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.2550732471976733 Normalized VI=0.9335050212554415'
'Chisquare statistics=None pvalue=None'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.0447401955291165 Normalized VI=0.9457395210645372'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[49 9] [ 4 5]]
'chi2 statistic: 5.3279'
'p-value: 0.020987'
'degrees of freedom: 1'
'expected frequencies:'
array([[45.88059701, 12.11940299], [ 7.11940299, 1.88059701]])
'Chisquare statistics=5.327882470489822 pvalue=0.020986868383295398'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.9792531048340005 Normalized VI=0.8873364616826944'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[48 10] [ 2 7]]
'chi2 statistic: 12.051'
'p-value: 0.00051765'
'degrees of freedom: 1'
'expected frequencies:'
array([[43.28358209, 14.71641791], [ 6.71641791, 2.28358209]])
'Chisquare statistics=12.050977574938024 pvalue=0.0005176522596520948'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.314490766651947 Normalized VI=0.9697874454976867'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[18 40] [ 6 3]]
'chi2 statistic: 2.8924'
'p-value: 0.088996'
'degrees of freedom: 1'
'expected frequencies:'
array([[20.7761194, 37.2238806], [ 3.2238806, 5.7761194]])
'Chisquare statistics=2.89243954008138 pvalue=0.0889960735982675'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.03506464305091 Normalized VI=0.9154811697521652'
'Chisquare statistics=None pvalue=None'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.457486397423024 Normalized VI=0.7976174117204141'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[55 3] [ 3 6]]
'chi2 statistic: 20.324'
'p-value: 6.5375e-06'
'degrees of freedom: 1'
'expected frequencies:'
array([[50.20895522, 7.79104478], [ 7.79104478, 1.20895522]])
'Chisquare statistics=20.324014437544957 pvalue=6.53749022744303e-06'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.5830206184100462 Normalized VI=0.7976174117204141'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[55 3] [ 3 6]]
'chi2 statistic: 20.324'
'p-value: 6.5375e-06'
'degrees of freedom: 1'
'expected frequencies:'
array([[50.20895522, 7.79104478], [ 7.79104478, 1.20895522]])
'Chisquare statistics=20.324014437544957 pvalue=6.53749022744303e-06'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044375.1', '15324213', '15325849', 'LOC115720716')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.1825790982358444 Normalized VI=0.9234846138056988'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[44 14] [ 2 7]]
'chi2 statistic: 8.0735'
'p-value: 0.0044918'
'degrees of freedom: 1'
'expected frequencies:'
array([[39.82089552, 18.17910448], [ 6.17910448, 2.82089552]])
'Chisquare statistics=8.073484587071544 pvalue=0.004491765563852945'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.2471454138247866 Normalized VI=0.9154811697521652'
'Chisquare statistics=None pvalue=None'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.1731763524897176 Normalized VI=0.9234846138056988'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[44 14] [ 2 7]]
'chi2 statistic: 8.0735'
'p-value: 0.0044918'
'degrees of freedom: 1'
'expected frequencies:'
array([[39.82089552, 18.17910448], [ 6.17910448, 2.82089552]])
'Chisquare statistics=8.073484587071544 pvalue=0.004491765563852945'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=0.7804303635511284 Normalized VI=2.220446049250313e-16'
'Chisquare statistics=None pvalue=None'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.4606094818501956 Normalized VI=0.995058147588618'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[28 30] [ 3 6]]
'chi2 statistic: 0.22775'
'p-value: 0.6332'
'degrees of freedom: 1'
'expected frequencies:'
array([[26.8358209, 31.1641791], [ 4.1641791, 4.8358209]])
'Chisquare statistics=0.22775091322319732 pvalue=0.633196530295906'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.1427421810098743 Normalized VI=0.9481912773993024'
'Chisquare statistics=None pvalue=None'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.2485606567132566 Normalized VI=0.9362915527482281'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[42 16] [ 2 7]]
'chi2 statistic: 6.6221'
'p-value: 0.010072'
'degrees of freedom: 1'
'expected frequencies:'
array([[38.08955224, 19.91044776], [ 5.91044776, 3.08955224]])
'Chisquare statistics=6.6221070336044106 pvalue=0.010072060681327441'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.9583563299546822 Normalized VI=0.8873364616826944'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[48 10] [ 2 7]]
'chi2 statistic: 12.051'
'p-value: 0.00051765'
'degrees of freedom: 1'
'expected frequencies:'
array([[43.28358209, 14.71641791], [ 6.71641791, 2.28358209]])
'Chisquare statistics=12.050977574938024 pvalue=0.0005176522596520948'
[('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.2566276011135336 Normalized VI=0.9302187453623346'
'Chisquare statistics=None pvalue=None'
[('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.4643525555318297 Normalized VI=0.9994853563310584'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[23 35] [ 4 5]]
'chi2 statistic: 0'
'p-value: 1'
'degrees of freedom: 1'
'expected frequencies:'
array([[23.37313433, 34.62686567], [ 3.62686567, 5.37313433]])
'Chisquare statistics=0.0 pvalue=1.0'
[('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.2454295610053174 Normalized VI=0.9366598417603532'
'Chisquare statistics=None pvalue=None'
[('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.4677225251093975 Normalized VI=0.9970259908992379'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[26 32] [ 3 6]]
'chi2 statistic: 0.081793'
'p-value: 0.77488'
'degrees of freedom: 1'
'expected frequencies:'
array([[25.10447761, 32.89552239], [ 3.89552239, 5.10447761]])
'Chisquare statistics=0.08179268275723003 pvalue=0.7748825634082139'
[('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.1618250558365117 Normalized VI=0.942621994145202'
'Chisquare statistics=None pvalue=None'
[('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.346015006525681 Normalized VI=0.9925422477603826'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[42 16] [ 5 4]]
'chi2 statistic: 0.40557'
'p-value: 0.52422'
'degrees of freedom: 1'
'expected frequencies:'
array([[40.68656716, 17.31343284], [ 6.31343284, 2.68656716]])
'Chisquare statistics=0.4055733879514142 pvalue=0.5242248731227908'
[('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.8738574734054136 Normalized VI=0.8366360064415539'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[48 10] [ 1 8]]
'chi2 statistic: 16.872'
'p-value: 3.9984e-05'
'degrees of freedom: 1'
'expected frequencies:'
array([[42.41791045, 15.58208955], [ 6.58208955, 2.41791045]])
'Chisquare statistics=16.872131323793884 pvalue=3.998436128556186e-05'
[('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.2566276011135336 Normalized VI=0.9302187453623346'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.1200464999411865 Normalized VI=0.9608881469533015'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.254082207390451 Normalized VI=0.9335050212554415'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.2575491618107812 Normalized VI=0.9302187453623346'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.254082207390451 Normalized VI=0.9335050212554415'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.255368391373318 Normalized VI=0.9231988659948347'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.240804124055667 Normalized VI=0.942621994145202'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.464622364889693 Normalized VI=0.995058147588618'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[28 30] [ 3 6]]
'chi2 statistic: 0.22775'
'p-value: 0.6332'
'degrees of freedom: 1'
'expected frequencies:'
array([[26.8358209, 31.1641791], [ 4.1641791, 4.8358209]])
'Chisquare statistics=0.22775091322319732 pvalue=0.633196530295906'
[('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.1157168153563997 Normalized VI=0.9194356121210085'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.8239681465378514 Normalized VI=0.9718422712933059'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[ 3 55] [ 2 7]]
'chi2 statistic: 1.2753'
'p-value: 0.25877'
'degrees of freedom: 1'
'expected frequencies:'
array([[ 4.32835821, 53.67164179], [ 0.67164179, 8.32835821]])
'Chisquare statistics=1.2753476084538373 pvalue=0.2587658642639437'
[('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.9695982766150801 Normalized VI=0.9560189026592211'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[51 7] [ 5 4]]
'chi2 statistic: 3.8256'
'p-value: 0.050475'
'degrees of freedom: 1'
'expected frequencies:'
array([[48.47761194, 9.52238806], [ 7.52238806, 1.47761194]])
'Chisquare statistics=3.8256230718515205 pvalue=0.05047457814685534'
[('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0268509360427631 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.2224583701312572 Normalized VI=0.9481912773993024'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.2917661357726784 Normalized VI=0.9878150173586462'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[19 39] [ 5 4]]
'chi2 statistic: 0.90919'
'p-value: 0.34033'
'degrees of freedom: 1'
'expected frequencies:'
array([[20.7761194, 37.2238806], [ 3.2238806, 5.7761194]])
'Chisquare statistics=0.9091945669607054 pvalue=0.34032821414357106'
[('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=0.7804303635511284 Normalized VI=2.220446049250313e-16'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.628854619493312 Normalized VI=0.7562159215696479'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[52 6] [ 1 8]]
'chi2 statistic: 24.521'
'p-value: 7.3521e-07'
'degrees of freedom: 1'
'expected frequencies:'
array([[45.88059701, 12.11940299], [ 7.11940299, 1.88059701]])
'Chisquare statistics=24.520558369736968 pvalue=7.352118200568794e-07'
[('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs cut: cluster_LOC115697762_LOC115696986.fam: No such file or directory Warning message: In system(paste0("cut -d \" \" -f2 ", bedfile_filtered, ".fam > ", : running command 'cut -d " " -f2 cluster_LOC115697762_LOC115696986.fam > cluster_LOC115697762_LOC115696986.iid' had status 1 cut: cluster_LOC115697762_LOC115696986.fam: No such file or directory Warning message: In system(paste0("cut -d \" \" -f2,3,4,5,6 ", bedfile_filtered, : running command 'cut -d " " -f2,3,4,5,6 cluster_LOC115697762_LOC115696986.fam > cluster_LOC115697762_LOC115696986.nofid' had status 1 mv: cannot stat ‘cluster_LOC115697762_LOC115696986.fam’: No such file or directory Warning message: In system(paste0("mv ", bedfile_filtered, ".fam ", bedfile_filtered, : running command 'mv cluster_LOC115697762_LOC115696986.fam cluster_LOC115697762_LOC115696986.fam.orig' had status 1 Error in read.table(paste(root, ".fam", sep = ""), as.is = T) : no lines available in input Calls: <Anonymous> ... .openGenoConnection -> .openPlinkConnection -> read.table Error: object 'Abed' not found Error: object 'A' not found Error: object 'AA' not found Error in mean(D_gene[D_gene > 0]) : object 'D_gene' not found Error: object 'mean_local' not found Error: object 'D_gene' not found Error: object 'Dtot' not found Error in as.dist(Dtot) : object 'Dtot' not found Calls: hclust -> as.dist Error: object 'hc' not found Error in head(ord_samples, 10) : object 'ord_samples' not found Error in nrow(tree$merge) : object 'hc' not found Calls: cutree -> nrow Error in is.data.frame(x) : object 'MAkgroup' not found Calls: write.table -> is.data.frame Error in as.phylo(hc) : object 'hc' not found Calls: write.tree -> as.phylo
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.4700915804131336 Normalized VI=0.9997918629399807'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[34 24] [ 5 4]]
'chi2 statistic: 0'
'p-value: 1'
'degrees of freedom: 1'
'expected frequencies:'
array([[33.76119403, 24.23880597], [ 5.23880597, 3.76119403]])
'Chisquare statistics=0.0 pvalue=1.0'
[('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.464622364889693 Normalized VI=0.995058147588618'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[28 30] [ 3 6]]
'chi2 statistic: 0.22775'
'p-value: 0.6332'
'degrees of freedom: 1'
'expected frequencies:'
array([[26.8358209, 31.1641791], [ 4.1641791, 4.8358209]])
'Chisquare statistics=0.22775091322319732 pvalue=0.633196530295906'
[('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.327258974460874 Normalized VI=0.9691857326857856'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[26 32] [ 1 8]]
'chi2 statistic: 2.4133'
'p-value: 0.12031'
'degrees of freedom: 1'
'expected frequencies:'
array([[23.37313433, 34.62686567], [ 3.62686567, 5.37313433]])
'Chisquare statistics=2.4132942209450823 pvalue=0.12030895621801667'
[('NC_044378.1', '34056091', '34061726', 'LOC115696986'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.406335635315915 Normalized VI=0.9878150173586462'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[19 39] [ 5 4]]
'chi2 statistic: 0.90919'
'p-value: 0.34033'
'degrees of freedom: 1'
'expected frequencies:'
array([[20.7761194, 37.2238806], [ 3.2238806, 5.7761194]])
'Chisquare statistics=0.9091945669607054 pvalue=0.34032821414357106'
[('NC_044378.1', '34056091', '34061726', 'LOC115696986'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.3753570458391793 Normalized VI=0.9997918629399807'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[34 24] [ 5 4]]
'chi2 statistic: 0'
'p-value: 1'
'degrees of freedom: 1'
'expected frequencies:'
array([[33.76119403, 24.23880597], [ 5.23880597, 3.76119403]])
'Chisquare statistics=0.0 pvalue=1.0'
[('NC_044378.1', '34132843', '34134661', 'LOC115697126'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.9216409342664442 Normalized VI=0.9467986228959275'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[52 6] [ 5 4]]
'chi2 statistic: 4.7018'
'p-value: 0.030131'
'degrees of freedom: 1'
'expected frequencies:'
array([[49.34328358, 8.65671642], [ 7.65671642, 1.34328358]])
'Chisquare statistics=4.701810680916851 pvalue=0.030130857973160327'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044375.1', '15324213', '15325849', 'LOC115720716')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.1689852462590586 Normalized VI=0.957437983536058'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[15 43] [ 6 3]]
'chi2 statistic: 4.2811'
'p-value: 0.038538'
'degrees of freedom: 1'
'expected frequencies:'
array([[18.17910448, 39.82089552], [ 2.82089552, 6.17910448]])
'Chisquare statistics=4.281106966358091 pvalue=0.03853824190347734'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.6080345137631373 Normalized VI=0.7976174117204141'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[55 3] [ 3 6]]
'chi2 statistic: 20.324'
'p-value: 6.5375e-06'
'degrees of freedom: 1'
'expected frequencies:'
array([[50.20895522, 7.79104478], [ 7.79104478, 1.20895522]])
'Chisquare statistics=20.324014437544957 pvalue=6.53749022744303e-06'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.2833917953093357 Normalized VI=0.9697874454976867'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[18 40] [ 6 3]]
'chi2 statistic: 2.8924'
'p-value: 0.088996'
'degrees of freedom: 1'
'expected frequencies:'
array([[20.7761194, 37.2238806], [ 3.2238806, 5.7761194]])
'Chisquare statistics=2.89243954008138 pvalue=0.0889960735982675'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.457486397423024 Normalized VI=0.7976174117204141'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[55 3] [ 3 6]]
'chi2 statistic: 20.324'
'p-value: 6.5375e-06'
'degrees of freedom: 1'
'expected frequencies:'
array([[50.20895522, 7.79104478], [ 7.79104478, 1.20895522]])
'Chisquare statistics=20.324014437544957 pvalue=6.53749022744303e-06'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.290316631308452 Normalized VI=0.9697874454976867'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[18 40] [ 6 3]]
'chi2 statistic: 2.8924'
'p-value: 0.088996'
'degrees of freedom: 1'
'expected frequencies:'
array([[20.7761194, 37.2238806], [ 3.2238806, 5.7761194]])
'Chisquare statistics=2.89243954008138 pvalue=0.0889960735982675'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.4521561458594703 Normalized VI=0.9930687369266393'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[36 22] [ 4 5]]
'chi2 statistic: 0.40672'
'p-value: 0.52364'
'degrees of freedom: 1'
'expected frequencies:'
array([[34.62686567, 23.37313433], [ 5.37313433, 3.62686567]])
'Chisquare statistics=0.40671695402298874 pvalue=0.5236405709247931'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.457486397423024 Normalized VI=0.7976174117204141'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[55 3] [ 3 6]]
'chi2 statistic: 20.324'
'p-value: 6.5375e-06'
'degrees of freedom: 1'
'expected frequencies:'
array([[50.20895522, 7.79104478], [ 7.79104478, 1.20895522]])
'Chisquare statistics=20.324014437544957 pvalue=6.53749022744303e-06'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.6752549736268594 Normalized VI=0.7990671477687583'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[53 5] [ 2 7]]
'chi2 statistic: 20.858'
'p-value: 4.9449e-06'
'degrees of freedom: 1'
'expected frequencies:'
array([[47.6119403, 10.3880597], [ 7.3880597, 1.6119403]])
'Chisquare statistics=20.858495152676184 pvalue=4.9449418523997585e-06'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.1872484974141786 Normalized VI=0.9466511884312888'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[13 45] [ 6 3]]
'chi2 statistic: 5.4896'
'p-value: 0.01913'
'degrees of freedom: 1'
'expected frequencies:'
array([[16.44776119, 41.55223881], [ 2.55223881, 6.44776119]])
'Chisquare statistics=5.48963742269947 pvalue=0.019129509769184892'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.237946133873143 Normalized VI=0.9660883539222911'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[17 41] [ 6 3]]
'chi2 statistic: 3.308'
'p-value: 0.068942'
'degrees of freedom: 1'
'expected frequencies:'
array([[19.91044776, 38.08955224], [ 3.08955224, 5.91044776]])
'Chisquare statistics=3.3080254380385563 pvalue=0.06894228413808544'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.6739937129553957 Normalized VI=0.8545350007770895'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[53 5] [ 3 6]]
'chi2 statistic: 15.134'
'p-value: 0.00010017'
'degrees of freedom: 1'
'expected frequencies:'
array([[48.47761194, 9.52238806], [ 7.52238806, 1.47761194]])
'Chisquare statistics=15.13356082375479 pvalue=0.00010016668741124936'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.296483561611032 Normalized VI=0.9731379933921644'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[19 39] [ 6 3]]
'chi2 statistic: 2.5172'
'p-value: 0.11261'
'degrees of freedom: 1'
'expected frequencies:'
array([[21.64179104, 36.35820896], [ 3.35820896, 5.64179104]])
'Chisquare statistics=2.51720625798212 pvalue=0.11260993126585218'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.406335635315915 Normalized VI=0.9878150173586462'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[39 19] [ 4 5]]
'chi2 statistic: 0.90919'
'p-value: 0.34033'
'degrees of freedom: 1'
'expected frequencies:'
array([[37.2238806, 20.7761194], [ 5.7761194, 3.2238806]])
'Chisquare statistics=0.9091945669607054 pvalue=0.34032821414357106'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.3107981652891505 Normalized VI=0.9731379933921644'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[19 39] [ 6 3]]
'chi2 statistic: 2.5172'
'p-value: 0.11261'
'degrees of freedom: 1'
'expected frequencies:'
array([[21.64179104, 36.35820896], [ 3.35820896, 5.64179104]])
'Chisquare statistics=2.51720625798212 pvalue=0.11260993126585218'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.6752549736268594 Normalized VI=0.7990671477687583'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[53 5] [ 2 7]]
'chi2 statistic: 20.858'
'p-value: 4.9449e-06'
'degrees of freedom: 1'
'expected frequencies:'
array([[47.6119403, 10.3880597], [ 7.3880597, 1.6119403]])
'Chisquare statistics=20.858495152676184 pvalue=4.9449418523997585e-06'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.2469516569491876 Normalized VI=0.9396951395329194'
'Chisquare statistics=None pvalue=None'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.6080345137631373 Normalized VI=0.7976174117204141'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[55 3] [ 3 6]]
'chi2 statistic: 20.324'
'p-value: 6.5375e-06'
'degrees of freedom: 1'
'expected frequencies:'
array([[50.20895522, 7.79104478], [ 7.79104478, 1.20895522]])
'Chisquare statistics=20.324014437544957 pvalue=6.53749022744303e-06'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.1513758607221156 Normalized VI=0.958453330375364'
'Chisquare statistics=None pvalue=None'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.2891495787903158 Normalized VI=0.9734778039278271'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[44 14] [ 4 5]]
'chi2 statistic: 2.3968'
'p-value: 0.12158'
'degrees of freedom: 1'
'expected frequencies:'
array([[41.55223881, 16.44776119], [ 6.44776119, 2.55223881]])
'Chisquare statistics=2.3967927631578947 pvalue=0.12158429406447033'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.2380799601548413 Normalized VI=0.942621994145202'
'Chisquare statistics=None pvalue=None'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.925534155908521 Normalized VI=0.8503592514120478'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[47 11] [ 1 8]]
'chi2 statistic: 15.466'
'p-value: 8.4005e-05'
'degrees of freedom: 1'
'expected frequencies:'
array([[41.55223881, 16.44776119], [ 6.44776119, 2.55223881]])
'Chisquare statistics=15.465947330611009 pvalue=8.400512871930317e-05'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.3038247042105047 Normalized VI=0.9731379933921644'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[19 39] [ 6 3]]
'chi2 statistic: 2.5172'
'p-value: 0.11261'
'degrees of freedom: 1'
'expected frequencies:'
array([[21.64179104, 36.35820896], [ 3.35820896, 5.64179104]])
'Chisquare statistics=2.51720625798212 pvalue=0.11260993126585218'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.094892935664378 Normalized VI=0.953033090659582'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[10 48] [ 5 4]]
'chi2 statistic: 4.5618'
'p-value: 0.032692'
'degrees of freedom: 1'
'expected frequencies:'
array([[12.98507463, 45.01492537], [ 2.01492537, 6.98507463]])
'Chisquare statistics=4.561820291777189 pvalue=0.03269230889928852'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.4367292262395766 Normalized VI=0.9915273500835595'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[37 21] [ 4 5]]
'chi2 statistic: 0.5486'
'p-value: 0.45889'
'degrees of freedom: 1'
'expected frequencies:'
array([[35.49253731, 22.50746269], [ 5.50746269, 3.49253731]])
'Chisquare statistics=0.5485985314097174 pvalue=0.4588908994827381'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.0447401955291165 Normalized VI=0.9457395210645372'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[ 9 49] [ 5 4]]
'chi2 statistic: 5.3279'
'p-value: 0.020987'
'degrees of freedom: 1'
'expected frequencies:'
array([[12.11940299, 45.88059701], [ 1.88059701, 7.11940299]])
'Chisquare statistics=5.327882470489823 pvalue=0.020986868383295387'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.4952803050430012 Normalized VI=0.7534182057846117'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[56 2] [ 3 6]]
'chi2 statistic: 23.906'
'p-value: 1.0114e-06'
'degrees of freedom: 1'
'expected frequencies:'
array([[51.07462687, 6.92537313], [ 7.92537313, 1.07462687]])
'Chisquare statistics=23.906263190791616 pvalue=1.0114216735861473e-06'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.1175271890736305 Normalized VI=0.953033090659582'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[10 48] [ 5 4]]
'chi2 statistic: 4.5618'
'p-value: 0.032692'
'degrees of freedom: 1'
'expected frequencies:'
array([[12.98507463, 45.01492537], [ 2.01492537, 6.98507463]])
'Chisquare statistics=4.561820291777189 pvalue=0.03269230889928852'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.4367292262395766 Normalized VI=0.9915273500835595'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[37 21] [ 4 5]]
'chi2 statistic: 0.5486'
'p-value: 0.45889'
'degrees of freedom: 1'
'expected frequencies:'
array([[35.49253731, 22.50746269], [ 5.50746269, 3.49253731]])
'Chisquare statistics=0.5485985314097174 pvalue=0.4588908994827381'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.4811947199301059 Normalized VI=0.7976174117204141'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[55 3] [ 3 6]]
'chi2 statistic: 20.324'
'p-value: 6.5375e-06'
'degrees of freedom: 1'
'expected frequencies:'
array([[50.20895522, 7.79104478], [ 7.79104478, 1.20895522]])
'Chisquare statistics=20.324014437544957 pvalue=6.53749022744303e-06'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.617281525300895 Normalized VI=0.9577782651531234'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[56 2] [ 7 2]]
'chi2 statistic: 2.119'
'p-value: 0.14549'
'degrees of freedom: 1'
'expected frequencies:'
array([[54.53731343, 3.46268657], [ 8.46268657, 0.53731343]])
'Chisquare statistics=2.1189620963327855 pvalue=0.145485106904391'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.4366061704682704 Normalized VI=0.9990338153257551'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[36 22] [ 5 4]]
'chi2 statistic: 3.0101e-05'
'p-value: 0.99562'
'degrees of freedom: 1'
'expected frequencies:'
array([[35.49253731, 22.50746269], [ 5.50746269, 3.49253731]])
'Chisquare statistics=3.0101428335238903e-05 pvalue=0.9956224467819879'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.4629676915304306 Normalized VI=0.9985054281112168'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[34 24] [ 6 3]]
'chi2 statistic: 0.0085865'
'p-value: 0.92617'
'degrees of freedom: 1'
'expected frequencies:'
array([[34.62686567, 23.37313433], [ 5.37313433, 3.62686567]])
'Chisquare statistics=0.00858654391939829 pvalue=0.9261708105906848'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.7839063491678404 Normalized VI=0.9201612548594424'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[54 4] [ 5 4]]
'chi2 statistic: 7.1807'
'p-value: 0.007369'
'degrees of freedom: 1'
'expected frequencies:'
array([[51.07462687, 6.92537313], [ 7.92537313, 1.07462687]])
'Chisquare statistics=7.18073718260926 pvalue=0.007369042346771813'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.4721090062853914 Normalized VI=0.996639918233424'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[25 33] [ 5 4]]
'chi2 statistic: 0.11474'
'p-value: 0.73481'
'degrees of freedom: 1'
'expected frequencies:'
array([[25.97014925, 32.02985075], [ 4.02985075, 4.97014925]])
'Chisquare statistics=0.11473671947809891 pvalue=0.7348145769900525'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.4721090062853914 Normalized VI=0.996639918233424'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[25 33] [ 5 4]]
'chi2 statistic: 0.11474'
'p-value: 0.73481'
'degrees of freedom: 1'
'expected frequencies:'
array([[25.97014925, 32.02985075], [ 4.02985075, 4.97014925]])
'Chisquare statistics=0.11473671947809891 pvalue=0.7348145769900525'
[('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.61555074820182 Normalized VI=0.768445009130241'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[54 4] [ 2 7]]
'chi2 statistic: 23.594'
'p-value: 1.1898e-06'
'degrees of freedom: 1'
'expected frequencies:'
array([[48.47761194, 9.52238806], [ 7.52238806, 1.47761194]])
'Chisquare statistics=23.593573512215755 pvalue=1.1898423283211327e-06'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.1148834791868323 Normalized VI=0.9075906351647957'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[46 12] [ 2 7]]
'chi2 statistic: 9.846'
'p-value: 0.001702'
'degrees of freedom: 1'
'expected frequencies:'
array([[41.55223881, 16.44776119], [ 6.44776119, 2.55223881]])
'Chisquare statistics=9.846022278517175 pvalue=0.0017019938167317026'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.179168295518212 Normalized VI=0.9402157161270285'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[46 12] [ 3 6]]
'chi2 statistic: 6.2055'
'p-value: 0.012735'
'degrees of freedom: 1'
'expected frequencies:'
array([[42.41791045, 15.58208955], [ 6.58208955, 2.41791045]])
'Chisquare statistics=6.20548637718178 pvalue=0.012735495035472312'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.2762964368770082 Normalized VI=0.9418043078502389'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[41 17] [ 2 7]]
'chi2 statistic: 5.9923'
'p-value: 0.014368'
'degrees of freedom: 1'
'expected frequencies:'
array([[37.2238806, 20.7761194], [ 5.7761194, 3.2238806]])
'Chisquare statistics=5.992301430841426 pvalue=0.014368444178495662'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0268509360427631 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.3075918049794937 Normalized VI=0.9619916910323038'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[42 16] [ 3 6]]
'chi2 statistic: 3.7689'
'p-value: 0.052213'
'degrees of freedom: 1'
'expected frequencies:'
array([[38.95522388, 19.04477612], [ 6.04477612, 2.95522388]])
'Chisquare statistics=3.768928267347807 pvalue=0.052213077586652085'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.4585360981523934 Normalized VI=0.994425265418426'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[35 23] [ 4 5]]
'chi2 statistic: 0.288'
'p-value: 0.59151'
'degrees of freedom: 1'
'expected frequencies:'
array([[33.76119403, 24.23880597], [ 5.23880597, 3.76119403]])
'Chisquare statistics=0.2879997158014397 pvalue=0.5915052199301791'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.1460779972899195 Normalized VI=0.9159892242176799'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[45 13] [ 2 7]]
'chi2 statistic: 8.9137'
'p-value: 0.0028304'
'degrees of freedom: 1'
'expected frequencies:'
array([[40.68656716, 17.31343284], [ 6.31343284, 2.68656716]])
'Chisquare statistics=8.91370496046303 pvalue=0.0028303845393122043'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.757581230280416 Normalized VI=0.8027830092893009'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[50 8] [ 1 8]]
'chi2 statistic: 20.216'
'p-value: 6.9177e-06'
'degrees of freedom: 1'
'expected frequencies:'
array([[44.14925373, 13.85074627], [ 6.85074627, 2.14925373]])
'Chisquare statistics=20.21587115449628 pvalue=6.917661865146827e-06'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.2197060540262226 Normalized VI=0.9481912773993024'
'Chisquare statistics=None pvalue=None'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.1720550700178984 Normalized VI=0.9559750710255214'
'Chisquare statistics=None pvalue=None'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.1720550700178984 Normalized VI=0.9559750710255214'
'Chisquare statistics=None pvalue=None'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.3137669830257632 Normalized VI=0.9770892617001078'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[15 43] [ 5 4]]
'chi2 statistic: 2.0157'
'p-value: 0.15568'
'degrees of freedom: 1'
'expected frequencies:'
array([[17.31343284, 40.68656716], [ 2.68656716, 6.31343284]])
'Chisquare statistics=2.015714416727806 pvalue=0.15567797818363338'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.2545951053999933 Normalized VI=0.9231988659948347'
'Chisquare statistics=None pvalue=None'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.8995728493074175 Normalized VI=0.8366360064415539'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[48 10] [ 1 8]]
'chi2 statistic: 16.872'
'p-value: 3.9984e-05'
'degrees of freedom: 1'
'expected frequencies:'
array([[42.41791045, 15.58208955], [ 6.58208955, 2.41791045]])
'Chisquare statistics=16.872131323793884 pvalue=3.998436128556186e-05'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.3212134072611796 Normalized VI=0.9514221363881161'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[39 19] [ 2 7]]
'chi2 statistic: 4.8887'
'p-value: 0.027032'
'degrees of freedom: 1'
'expected frequencies:'
array([[35.49253731, 22.50746269], [ 5.50746269, 3.49253731]])
'Chisquare statistics=4.88874287449771 pvalue=0.02703236273085614'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.464622364889693 Normalized VI=0.995058147588618'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[28 30] [ 3 6]]
'chi2 statistic: 0.22775'
'p-value: 0.6332'
'degrees of freedom: 1'
'expected frequencies:'
array([[26.8358209, 31.1641791], [ 4.1641791, 4.8358209]])
'Chisquare statistics=0.22775091322319732 pvalue=0.633196530295906'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.4689182455513246 Normalized VI=0.9956116413788935'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[34 24] [ 4 5]]
'chi2 statistic: 0.19104'
'p-value: 0.66205'
'degrees of freedom: 1'
'expected frequencies:'
array([[32.89552239, 25.10447761], [ 5.10447761, 3.89552239]])
'Chisquare statistics=0.19104371362413158 pvalue=0.6620493597769073'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.2659708599156305 Normalized VI=0.9418043078502389'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[41 17] [ 2 7]]
'chi2 statistic: 5.9923'
'p-value: 0.014368'
'degrees of freedom: 1'
'expected frequencies:'
array([[37.2238806, 20.7761194], [ 5.7761194, 3.2238806]])
'Chisquare statistics=5.992301430841426 pvalue=0.014368444178495662'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.0339923602019816 Normalized VI=0.9634871374563486'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[50 8] [ 5 4]]
'chi2 statistic: 3.112'
'p-value: 0.077717'
'degrees of freedom: 1'
'expected frequencies:'
array([[47.6119403, 10.3880597], [ 7.3880597, 1.6119403]])
'Chisquare statistics=3.1120130906768835 pvalue=0.0777168486939795'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.349231032019524 Normalized VI=0.9608388685749721'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[29 29] [ 1 8]]
'chi2 statistic: 3.3222'
'p-value: 0.068352'
'degrees of freedom: 1'
'expected frequencies:'
array([[25.97014925, 32.02985075], [ 4.02985075, 4.97014925]])
'Chisquare statistics=3.3221613855234535 pvalue=0.06835191259985095'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.479098171706006 Normalized VI=0.9975198529351784'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[26 32] [ 5 4]]
'chi2 statistic: 0.058224'
'p-value: 0.80932'
'degrees of freedom: 1'
'expected frequencies:'
array([[26.8358209, 31.1641791], [ 4.1641791, 4.8358209]])
'Chisquare statistics=0.0582244160177975 pvalue=0.8093246567458723'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.2485606567132566 Normalized VI=0.9362915527482281'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[42 16] [ 2 7]]
'chi2 statistic: 6.6221'
'p-value: 0.010072'
'degrees of freedom: 1'
'expected frequencies:'
array([[38.08955224, 19.91044776], [ 5.91044776, 3.08955224]])
'Chisquare statistics=6.6221070336044106 pvalue=0.010072060681327441'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.5974895051917077 Normalized VI=0.7255215078837542'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[53 5] [ 1 8]]
'chi2 statistic: 27.172'
'p-value: 1.8617e-07'
'degrees of freedom: 1'
'expected frequencies:'
array([[46.74626866, 11.25373134], [ 7.25373134, 1.74626866]])
'Chisquare statistics=27.171646281560076 pvalue=1.861690301418998e-07'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0268509360427631 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.410508068298428 Normalized VI=0.9976553100683083'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[38 20] [ 5 4]]
'chi2 statistic: 0.042567'
'p-value: 0.83654'
'degrees of freedom: 1'
'expected frequencies:'
array([[37.2238806, 20.7761194], [ 5.7761194, 3.2238806]])
'Chisquare statistics=0.042566511479402366 pvalue=0.8365436654620396'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.464622364889693 Normalized VI=0.995058147588618'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[28 30] [ 3 6]]
'chi2 statistic: 0.22775'
'p-value: 0.6332'
'degrees of freedom: 1'
'expected frequencies:'
array([[26.8358209, 31.1641791], [ 4.1641791, 4.8358209]])
'Chisquare statistics=0.22775091322319732 pvalue=0.633196530295906'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.983926490517206 Normalized VI=0.9560189026592211'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[51 7] [ 5 4]]
'chi2 statistic: 3.8256'
'p-value: 0.050475'
'degrees of freedom: 1'
'expected frequencies:'
array([[48.47761194, 9.52238806], [ 7.52238806, 1.47761194]])
'Chisquare statistics=3.8256230718515205 pvalue=0.05047457814685534'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.4721090062853914 Normalized VI=0.996639918233424'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[25 33] [ 5 4]]
'chi2 statistic: 0.11474'
'p-value: 0.73481'
'degrees of freedom: 1'
'expected frequencies:'
array([[25.97014925, 32.02985075], [ 4.02985075, 4.97014925]])
'Chisquare statistics=0.11473671947809891 pvalue=0.7348145769900525'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.475010271735181 Normalized VI=0.996639918233424'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[25 33] [ 5 4]]
'chi2 statistic: 0.11474'
'p-value: 0.73481'
'degrees of freedom: 1'
'expected frequencies:'
array([[25.97014925, 32.02985075], [ 4.02985075, 4.97014925]])
'Chisquare statistics=0.11473671947809891 pvalue=0.7348145769900525'
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.8116272188243454 Normalized VI=0.8437365688439276'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[51 7] [ 2 7]]
'chi2 statistic: 16.57'
'p-value: 4.6888e-05'
'degrees of freedom: 1'
'expected frequencies:'
array([[45.88059701, 12.11940299], [ 7.11940299, 1.88059701]])
'Chisquare statistics=16.569969198913572 pvalue=4.688763615957685e-05'
[('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.206122434602688 Normalized VI=0.9508528447712243'
'Chisquare statistics=None pvalue=None'
[('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.192403148490312 Normalized VI=0.9534444998582267'
'Chisquare statistics=None pvalue=None'
[('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.4643329145552677 Normalized VI=0.9970259908992379'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[26 32] [ 3 6]]
'chi2 statistic: 0.081793'
'p-value: 0.77488'
'degrees of freedom: 1'
'expected frequencies:'
array([[25.10447761, 32.89552239], [ 3.89552239, 5.10447761]])
'Chisquare statistics=0.08179268275723003 pvalue=0.7748825634082139'
[('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.4689182455513246 Normalized VI=0.9956116413788935'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[34 24] [ 4 5]]
'chi2 statistic: 0.19104'
'p-value: 0.66205'
'degrees of freedom: 1'
'expected frequencies:'
array([[32.89552239, 25.10447761], [ 5.10447761, 3.89552239]])
'Chisquare statistics=0.19104371362413158 pvalue=0.6620493597769073'
[('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.1720550700178984 Normalized VI=0.9559750710255214'
'Chisquare statistics=None pvalue=None'
[('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.6730204211370165 Normalized VI=0.7562159215696479'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[52 6] [ 1 8]]
'chi2 statistic: 24.521'
'p-value: 7.3521e-07'
'degrees of freedom: 1'
'expected frequencies:'
array([[45.88059701, 12.11940299], [ 7.11940299, 1.88059701]])
'Chisquare statistics=24.520558369736968 pvalue=7.352118200568794e-07'
[('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.72041759569365 Normalized VI=0.8533418420794352'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[55 3] [ 4 5]]
'chi2 statistic: 14.323'
'p-value: 0.00015399'
'degrees of freedom: 1'
'expected frequencies:'
array([[51.07462687, 6.92537313], [ 7.92537313, 1.07462687]])
'Chisquare statistics=14.322791861484513 pvalue=0.0001539891438858937'
[('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.366158077310185 Normalized VI=0.9665441116365383'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[27 31] [ 1 8]]
'chi2 statistic: 2.6978'
'p-value: 0.10049'
'degrees of freedom: 1'
'expected frequencies:'
array([[24.23880597, 33.76119403], [ 3.76119403, 5.23880597]])
'Chisquare statistics=2.697782461791083 pvalue=0.10048792566576453'
[('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.4750732313633135 Normalized VI=0.9997918629399807'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[34 24] [ 5 4]]
'chi2 statistic: 0'
'p-value: 1'
'degrees of freedom: 1'
'expected frequencies:'
array([[33.76119403, 24.23880597], [ 5.23880597, 3.76119403]])
'Chisquare statistics=0.0 pvalue=1.0'
[('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.5530749319028465 Normalized VI=0.8261007402007382'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[57 1] [ 5 4]]
'chi2 statistic: 14.868'
'p-value: 0.00011528'
'degrees of freedom: 1'
'expected frequencies:'
array([[53.67164179, 4.32835821], [ 8.32835821, 0.67164179]])
'Chisquare statistics=14.868290384377703 pvalue=0.00011528471926069631'
[('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.8807752952214551 Normalized VI=0.8366360064415539'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[48 10] [ 1 8]]
'chi2 statistic: 16.872'
'p-value: 3.9984e-05'
'degrees of freedom: 1'
'expected frequencies:'
array([[42.41791045, 15.58208955], [ 6.58208955, 2.41791045]])
'Chisquare statistics=16.872131323793884 pvalue=3.998436128556186e-05'
[('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.361805990234039 Normalized VI=0.9691857326857856'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[26 32] [ 1 8]]
'chi2 statistic: 2.4133'
'p-value: 0.12031'
'degrees of freedom: 1'
'expected frequencies:'
array([[23.37313433, 34.62686567], [ 3.62686567, 5.37313433]])
'Chisquare statistics=2.4132942209450823 pvalue=0.12030895621801667'
[('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.4750732313633135 Normalized VI=0.9997918629399807'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[34 24] [ 5 4]]
'chi2 statistic: 0'
'p-value: 1'
'degrees of freedom: 1'
'expected frequencies:'
array([[33.76119403, 24.23880597], [ 5.23880597, 3.76119403]])
'Chisquare statistics=0.0 pvalue=1.0'
[('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.6298789621039458 Normalized VI=0.768445009130241'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[54 4] [ 2 7]]
'chi2 statistic: 23.594'
'p-value: 1.1898e-06'
'degrees of freedom: 1'
'expected frequencies:'
array([[48.47761194, 9.52238806], [ 7.52238806, 1.47761194]])
'Chisquare statistics=23.593573512215755 pvalue=1.1898423283211327e-06'
[('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.8936336927304303 Normalized VI=0.8366360064415539'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[48 10] [ 1 8]]
'chi2 statistic: 16.872'
'p-value: 3.9984e-05'
'degrees of freedom: 1'
'expected frequencies:'
array([[42.41791045, 15.58208955], [ 6.58208955, 2.41791045]])
'Chisquare statistics=16.872131323793884 pvalue=3.998436128556186e-05'
[('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.448680648595246 Normalized VI=0.9930687369266393'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[36 22] [ 4 5]]
'chi2 statistic: 0.40672'
'p-value: 0.52364'
'degrees of freedom: 1'
'expected frequencies:'
array([[34.62686567, 23.37313433], [ 5.37313433, 3.62686567]])
'Chisquare statistics=0.40671695402298874 pvalue=0.5236405709247931'
[('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.4537069405126606 Normalized VI=0.9925795514915444'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[30 28] [ 3 6]]
'chi2 statistic: 0.44686'
'p-value: 0.50383'
'degrees of freedom: 1'
'expected frequencies:'
array([[28.56716418, 29.43283582], [ 4.43283582, 4.56716418]])
'Chisquare statistics=0.44685999617541183 pvalue=0.5038298761990317'
[('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.8738574734054136 Normalized VI=0.8366360064415539'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[48 10] [ 1 8]]
'chi2 statistic: 16.872'
'p-value: 3.9984e-05'
'degrees of freedom: 1'
'expected frequencies:'
array([[42.41791045, 15.58208955], [ 6.58208955, 2.41791045]])
'Chisquare statistics=16.872131323793884 pvalue=3.998436128556186e-05'
[('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.4721090062853914 Normalized VI=0.996639918233424'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[25 33] [ 5 4]]
'chi2 statistic: 0.11474'
'p-value: 0.73481'
'degrees of freedom: 1'
'expected frequencies:'
array([[25.97014925, 32.02985075], [ 4.02985075, 4.97014925]])
'Chisquare statistics=0.11473671947809891 pvalue=0.7348145769900525'
[('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.4663350547537473 Normalized VI=0.9956116413788935'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[34 24] [ 4 5]]
'chi2 statistic: 0.19104'
'p-value: 0.66205'
'degrees of freedom: 1'
'expected frequencies:'
array([[32.89552239, 25.10447761], [ 5.10447761, 3.89552239]])
'Chisquare statistics=0.19104371362413158 pvalue=0.6620493597769073'
[('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.925534155908521 Normalized VI=0.8503592514120478'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[47 11] [ 1 8]]
'chi2 statistic: 15.466'
'p-value: 8.4005e-05'
'degrees of freedom: 1'
'expected frequencies:'
array([[41.55223881, 16.44776119], [ 6.44776119, 2.55223881]])
'Chisquare statistics=15.465947330611009 pvalue=8.400512871930317e-05'
[('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.1543819307996195 Normalized VI=0.958453330375364'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.4677225251093975 Normalized VI=0.9970259908992379'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[26 32] [ 3 6]]
'chi2 statistic: 0.081793'
'p-value: 0.77488'
'degrees of freedom: 1'
'expected frequencies:'
array([[25.10447761, 32.89552239], [ 3.89552239, 5.10447761]])
'Chisquare statistics=0.08179268275723003 pvalue=0.7748825634082139'
[('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.3116201639939407 Normalized VI=0.9770892617001078'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[15 43] [ 5 4]]
'chi2 statistic: 2.0157'
'p-value: 0.15568'
'degrees of freedom: 1'
'expected frequencies:'
array([[17.31343284, 40.68656716], [ 2.68656716, 6.31343284]])
'Chisquare statistics=2.015714416727806 pvalue=0.15567797818363338'
[('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.1720550700178984 Normalized VI=0.9559750710255214'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.2487699424897656 Normalized VI=0.9194356121210085'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.4833662474034088 Normalized VI=0.6426721281076389'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.4606094818501956 Normalized VI=0.995058147588618'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[28 30] [ 3 6]]
'chi2 statistic: 0.22775'
'p-value: 0.6332'
'degrees of freedom: 1'
'expected frequencies:'
array([[26.8358209, 31.1641791], [ 4.1641791, 4.8358209]])
'Chisquare statistics=0.22775091322319732 pvalue=0.633196530295906'
[('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.3154265592514505 Normalized VI=0.9770892617001078'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[15 43] [ 5 4]]
'chi2 statistic: 2.0157'
'p-value: 0.15568'
'degrees of freedom: 1'
'expected frequencies:'
array([[17.31343284, 40.68656716], [ 2.68656716, 6.31343284]])
'Chisquare statistics=2.015714416727806 pvalue=0.15567797818363338'
[('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.2574354325871373 Normalized VI=0.9267880706034901'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.9051835017634857 Normalized VI=0.8366360064415539'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[48 10] [ 1 8]]
'chi2 statistic: 16.872'
'p-value: 3.9984e-05'
'degrees of freedom: 1'
'expected frequencies:'
array([[42.41791045, 15.58208955], [ 6.58208955, 2.41791045]])
'Chisquare statistics=16.872131323793884 pvalue=3.998436128556186e-05'
[('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.4833662474034088 Normalized VI=0.6426721281076389'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.3600625407703935 Normalized VI=0.9925422477603826'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[42 16] [ 5 4]]
'chi2 statistic: 0.40557'
'p-value: 0.52422'
'degrees of freedom: 1'
'expected frequencies:'
array([[40.68656716, 17.31343284], [ 6.31343284, 2.68656716]])
'Chisquare statistics=0.4055733879514142 pvalue=0.5242248731227908'
[('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.4677225251093975 Normalized VI=0.9970259908992379'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[26 32] [ 3 6]]
'chi2 statistic: 0.081793'
'p-value: 0.77488'
'degrees of freedom: 1'
'expected frequencies:'
array([[25.10447761, 32.89552239], [ 3.89552239, 5.10447761]])
'Chisquare statistics=0.08179268275723003 pvalue=0.7748825634082139'
[('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.2574993920683073 Normalized VI=0.9267880706034901'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.403255845249613 Normalized VI=0.9878150173586462'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[19 39] [ 5 4]]
'chi2 statistic: 0.90919'
'p-value: 0.34033'
'degrees of freedom: 1'
'expected frequencies:'
array([[20.7761194, 37.2238806], [ 3.2238806, 5.7761194]])
'Chisquare statistics=0.9091945669607054 pvalue=0.34032821414357106'
[('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.189062412695028 Normalized VI=0.959279712382977'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[11 47] [ 5 4]]
'chi2 statistic: 3.9019'
'p-value: 0.048232'
'degrees of freedom: 1'
'expected frequencies:'
array([[13.85074627, 44.14925373], [ 2.14925373, 6.85074627]])
'Chisquare statistics=3.901892114604462 pvalue=0.048231758510510474'
[('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.9497792613951526 Normalized VI=0.8503592514120478'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[47 11] [ 1 8]]
'chi2 statistic: 15.466'
'p-value: 8.4005e-05'
'degrees of freedom: 1'
'expected frequencies:'
array([[41.55223881, 16.44776119], [ 6.44776119, 2.55223881]])
'Chisquare statistics=15.465947330611009 pvalue=8.400512871930317e-05'
[('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.464063315671795 Normalized VI=0.993885008428136'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[29 29] [ 3 6]]
'chi2 statistic: 0.32802'
'p-value: 0.56683'
'degrees of freedom: 1'
'expected frequencies:'
array([[27.70149254, 30.29850746], [ 4.29850746, 4.70149254]])
'Chisquare statistics=0.3280151033114397 pvalue=0.566830211256313'
[('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.46079740802292 Normalized VI=0.994425265418426'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[35 23] [ 4 5]]
'chi2 statistic: 0.288'
'p-value: 0.59151'
'degrees of freedom: 1'
'expected frequencies:'
array([[33.76119403, 24.23880597], [ 5.23880597, 3.76119403]])
'Chisquare statistics=0.2879997158014397 pvalue=0.5915052199301791'
[('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.5030899941515585 Normalized VI=0.8261007402007382'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[57 1] [ 5 4]]
'chi2 statistic: 14.868'
'p-value: 0.00011528'
'degrees of freedom: 1'
'expected frequencies:'
array([[53.67164179, 4.32835821], [ 8.32835821, 0.67164179]])
'Chisquare statistics=14.868290384377703 pvalue=0.00011528471926069631'
[('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.8389205097076224 Normalized VI=0.8209372390504586'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[49 9] [ 1 8]]
'chi2 statistic: 18.445'
'p-value: 1.7487e-05'
'degrees of freedom: 1'
'expected frequencies:'
array([[43.28358209, 14.71641791], [ 6.71641791, 2.28358209]])
'Chisquare statistics=18.445045638945235 pvalue=1.748748789304477e-05'
[('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.462335980888164 Normalized VI=0.9990338153257551'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[36 22] [ 5 4]]
'chi2 statistic: 3.0101e-05'
'p-value: 0.99562'
'degrees of freedom: 1'
'expected frequencies:'
array([[35.49253731, 22.50746269], [ 5.50746269, 3.49253731]])
'Chisquare statistics=3.0101428335238903e-05 pvalue=0.9956224467819879'
[('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.464622364889693 Normalized VI=0.995058147588618'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[28 30] [ 3 6]]
'chi2 statistic: 0.22775'
'p-value: 0.6332'
'degrees of freedom: 1'
'expected frequencies:'
array([[26.8358209, 31.1641791], [ 4.1641791, 4.8358209]])
'Chisquare statistics=0.22775091322319732 pvalue=0.633196530295906'
[('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.8180237348283041 Normalized VI=0.8209372390504586'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[49 9] [ 1 8]]
'chi2 statistic: 18.445'
'p-value: 1.7487e-05'
'degrees of freedom: 1'
'expected frequencies:'
array([[43.28358209, 14.71641791], [ 6.71641791, 2.28358209]])
'Chisquare statistics=18.445045638945235 pvalue=1.748748789304477e-05'
[('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.4811996921154216 Normalized VI=0.9982591783754817'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[27 31] [ 5 4]]
'chi2 statistic: 0.020886'
'p-value: 0.88509'
'degrees of freedom: 1'
'expected frequencies:'
array([[27.70149254, 30.29850746], [ 4.29850746, 4.70149254]])
'Chisquare statistics=0.02088592980295562 pvalue=0.8850901393264404'
[('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.475010271735181 Normalized VI=0.996639918233424'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[25 33] [ 5 4]]
'chi2 statistic: 0.11474'
'p-value: 0.73481'
'degrees of freedom: 1'
'expected frequencies:'
array([[25.97014925, 32.02985075], [ 4.02985075, 4.97014925]])
'Chisquare statistics=0.11473671947809891 pvalue=0.7348145769900525'
[('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.229598207175779 Normalized VI=0.9192567723878957'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[39 19] [ 1 8]]
'chi2 statistic: 8.003'
'p-value: 0.0046699'
'degrees of freedom: 1'
'expected frequencies:'
array([[34.62686567, 23.37313433], [ 5.37313433, 3.62686567]])
'Chisquare statistics=8.00304517879949 pvalue=0.004669874881501615'
[('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.475627615470876 Normalized VI=0.6426721281076389'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.42118234373609 Normalized VI=0.9967013763097243'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[39 19] [ 5 4]]
'chi2 statistic: 0.095916'
'p-value: 0.75679'
'degrees of freedom: 1'
'expected frequencies:'
array([[38.08955224, 19.91044776], [ 5.91044776, 3.08955224]])
'Chisquare statistics=0.09591558387472929 pvalue=0.7567872685443906'
[('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.464063315671795 Normalized VI=0.993885008428136'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[29 29] [ 3 6]]
'chi2 statistic: 0.32802'
'p-value: 0.56683'
'degrees of freedom: 1'
'expected frequencies:'
array([[27.70149254, 30.29850746], [ 4.29850746, 4.70149254]])
'Chisquare statistics=0.3280151033114397 pvalue=0.566830211256313'
[('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.8322771019311712 Normalized VI=0.8209372390504586'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[49 9] [ 1 8]]
'chi2 statistic: 18.445'
'p-value: 1.7487e-05'
'degrees of freedom: 1'
'expected frequencies:'
array([[43.28358209, 14.71641791], [ 6.71641791, 2.28358209]])
'Chisquare statistics=18.445045638945235 pvalue=1.748748789304477e-05'
[('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.4689182455513246 Normalized VI=0.9956116413788935'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[34 24] [ 4 5]]
'chi2 statistic: 0.19104'
'p-value: 0.66205'
'degrees of freedom: 1'
'expected frequencies:'
array([[32.89552239, 25.10447761], [ 5.10447761, 3.89552239]])
'Chisquare statistics=0.19104371362413158 pvalue=0.6620493597769073'
[('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.435634198971208 Normalized VI=0.9976553100683083'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[38 20] [ 5 4]]
'chi2 statistic: 0.042567'
'p-value: 0.83654'
'degrees of freedom: 1'
'expected frequencies:'
array([[37.2238806, 20.7761194], [ 5.7761194, 3.2238806]])
'Chisquare statistics=0.042566511479402366 pvalue=0.8365436654620396'
[('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.715172647543898 Normalized VI=0.7815174993931131'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[51 7] [ 1 8]]
'chi2 statistic: 22.224'
'p-value: 2.4261e-06'
'degrees of freedom: 1'
'expected frequencies:'
array([[45.01492537, 12.98507463], [ 6.98507463, 2.01492537]])
'Chisquare statistics=22.22411030061892 pvalue=2.426080607735151e-06'
[('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0346707348843731 Normalized VI=0.26369637102311905'
'Chisquare statistics=None pvalue=None'
[('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.4797410854916353 Normalized VI=0.9996843637634807'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[30 28] [ 5 4]]
'chi2 statistic: 0'
'p-value: 1'
'degrees of freedom: 1'
'expected frequencies:'
array([[30.29850746, 27.70149254], [ 4.70149254, 4.29850746]])
'Chisquare statistics=0.0 pvalue=1.0'
[('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.4595245917524515 Normalized VI=0.9990338153257551'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[36 22] [ 5 4]]
'chi2 statistic: 3.0101e-05'
'p-value: 0.99562'
'degrees of freedom: 1'
'expected frequencies:'
array([[35.49253731, 22.50746269], [ 5.50746269, 3.49253731]])
'Chisquare statistics=3.0101428335238903e-05 pvalue=0.9956224467819879'
[('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.4537069405126606 Normalized VI=0.9925795514915444'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[30 28] [ 3 6]]
'chi2 statistic: 0.44686'
'p-value: 0.50383'
'degrees of freedom: 1'
'expected frequencies:'
array([[28.56716418, 29.43283582], [ 4.43283582, 4.56716418]])
'Chisquare statistics=0.44685999617541183 pvalue=0.5038298761990317'
[('NC_044378.1', '34056091', '34061726', 'LOC115696986'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')] group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=2.4663350547537473 Normalized VI=0.9956116413788935'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[34 24] [ 4 5]]
'chi2 statistic: 0.19104'
'p-value: 0.66205'
'degrees of freedom: 1'
'expected frequencies:'
array([[32.89552239, 25.10447761], [ 5.10447761, 3.89552239]])
'Chisquare statistics=0.19104371362413158 pvalue=0.6620493597769073'
LOC115717841 LOC115718836 LOC115720716 LOC115697880 LOC115696909 LOC115696884 LOC115697762 LOC115696987 LOC115696986 LOC115697126 LOC115697019 LOC115717841_LOC115718836 LOC115717841_LOC115720716 LOC115717841_LOC115697880 LOC115717841_LOC115696909 LOC115717841_LOC115696884 LOC115717841_LOC115697762 LOC115717841_LOC115696987 LOC115717841_LOC115696986 LOC115717841_LOC115697126 LOC115717841_LOC115697019 LOC115718836_LOC115720716 LOC115718836_LOC115697880 LOC115718836_LOC115696909 LOC115718836_LOC115696884 LOC115718836_LOC115697762 LOC115718836_LOC115696987 LOC115718836_LOC115696986 LOC115718836_LOC115697126 LOC115718836_LOC115697019 LOC115720716_LOC115697880 LOC115720716_LOC115696909 LOC115720716_LOC115696884 LOC115720716_LOC115697762 LOC115720716_LOC115696987 LOC115720716_LOC115696986 LOC115720716_LOC115697126 LOC115720716_LOC115697019 LOC115697880_LOC115696909 LOC115697880_LOC115696884 LOC115697880_LOC115697762 LOC115697880_LOC115696987 LOC115697880_LOC115696986 LOC115697880_LOC115697126 LOC115697880_LOC115697019 LOC115696909_LOC115696884 LOC115696909_LOC115697762 LOC115696909_LOC115696987 LOC115696909_LOC115696986 LOC115696909_LOC115697126 LOC115696909_LOC115697019 LOC115696884_LOC115697762 LOC115696884_LOC115696987 LOC115696884_LOC115696986 LOC115696884_LOC115697126 LOC115696884_LOC115697019 LOC115697762_LOC115696987 LOC115697762_LOC115696986 LOC115697762_LOC115697126 LOC115697762_LOC115697019 LOC115696987_LOC115696986 LOC115696987_LOC115697126 LOC115696987_LOC115697019 LOC115696986_LOC115697126 LOC115696986_LOC115697019 LOC115697126_LOC115697019 LOC115717841_LOC115718836_LOC115720716 LOC115717841_LOC115718836_LOC115697880 LOC115717841_LOC115718836_LOC115696909 LOC115717841_LOC115718836_LOC115696884 LOC115717841_LOC115718836_LOC115697762 LOC115717841_LOC115718836_LOC115696987 LOC115717841_LOC115718836_LOC115696986 LOC115717841_LOC115718836_LOC115697126 LOC115717841_LOC115718836_LOC115697019 LOC115717841_LOC115720716_LOC115697880 LOC115717841_LOC115720716_LOC115696909 LOC115717841_LOC115720716_LOC115696884 LOC115717841_LOC115720716_LOC115697762 LOC115717841_LOC115720716_LOC115696987 LOC115717841_LOC115720716_LOC115696986 LOC115717841_LOC115720716_LOC115697126 LOC115717841_LOC115720716_LOC115697019 LOC115717841_LOC115697880_LOC115696909 LOC115717841_LOC115697880_LOC115696884 LOC115717841_LOC115697880_LOC115697762 LOC115717841_LOC115697880_LOC115696987 LOC115717841_LOC115697880_LOC115696986 LOC115717841_LOC115697880_LOC115697126 LOC115717841_LOC115697880_LOC115697019 LOC115717841_LOC115696909_LOC115696884 LOC115717841_LOC115696909_LOC115697762 LOC115717841_LOC115696909_LOC115696987 LOC115717841_LOC115696909_LOC115696986 LOC115717841_LOC115696909_LOC115697126 LOC115717841_LOC115696909_LOC115697019 LOC115717841_LOC115696884_LOC115697762 LOC115717841_LOC115696884_LOC115696987 LOC115717841_LOC115696884_LOC115696986 LOC115717841_LOC115696884_LOC115697126 LOC115717841_LOC115696884_LOC115697019 LOC115717841_LOC115697762_LOC115696987 LOC115717841_LOC115697762_LOC115696986 LOC115717841_LOC115697762_LOC115697126 LOC115717841_LOC115697762_LOC115697019 LOC115717841_LOC115696987_LOC115696986 LOC115717841_LOC115696987_LOC115697126 LOC115717841_LOC115696987_LOC115697019 LOC115717841_LOC115696986_LOC115697126 LOC115717841_LOC115696986_LOC115697019 LOC115717841_LOC115697126_LOC115697019 LOC115718836_LOC115720716_LOC115697880 LOC115718836_LOC115720716_LOC115696909 LOC115718836_LOC115720716_LOC115696884 LOC115718836_LOC115720716_LOC115697762 LOC115718836_LOC115720716_LOC115696987 LOC115718836_LOC115720716_LOC115696986 LOC115718836_LOC115720716_LOC115697126 LOC115718836_LOC115720716_LOC115697019 LOC115718836_LOC115697880_LOC115696909 LOC115718836_LOC115697880_LOC115696884 LOC115718836_LOC115697880_LOC115697762 LOC115718836_LOC115697880_LOC115696987 LOC115718836_LOC115697880_LOC115696986 LOC115718836_LOC115697880_LOC115697126 LOC115718836_LOC115697880_LOC115697019 LOC115718836_LOC115696909_LOC115696884 LOC115718836_LOC115696909_LOC115697762 LOC115718836_LOC115696909_LOC115696987 LOC115718836_LOC115696909_LOC115696986 LOC115718836_LOC115696909_LOC115697126 LOC115718836_LOC115696909_LOC115697019 LOC115718836_LOC115696884_LOC115697762 LOC115718836_LOC115696884_LOC115696987 LOC115718836_LOC115696884_LOC115696986 LOC115718836_LOC115696884_LOC115697126 LOC115718836_LOC115696884_LOC115697019 LOC115718836_LOC115697762_LOC115696987 LOC115718836_LOC115697762_LOC115696986 LOC115718836_LOC115697762_LOC115697126 LOC115718836_LOC115697762_LOC115697019 LOC115718836_LOC115696987_LOC115696986 LOC115718836_LOC115696987_LOC115697126 LOC115718836_LOC115696987_LOC115697019 LOC115718836_LOC115696986_LOC115697126 LOC115718836_LOC115696986_LOC115697019 LOC115718836_LOC115697126_LOC115697019 LOC115720716_LOC115697880_LOC115696909 LOC115720716_LOC115697880_LOC115696884 LOC115720716_LOC115697880_LOC115697762 LOC115720716_LOC115697880_LOC115696987 LOC115720716_LOC115697880_LOC115696986 LOC115720716_LOC115697880_LOC115697126 LOC115720716_LOC115697880_LOC115697019 LOC115720716_LOC115696909_LOC115696884 LOC115720716_LOC115696909_LOC115697762 LOC115720716_LOC115696909_LOC115696987 LOC115720716_LOC115696909_LOC115696986 LOC115720716_LOC115696909_LOC115697126 LOC115720716_LOC115696909_LOC115697019 LOC115720716_LOC115696884_LOC115697762 LOC115720716_LOC115696884_LOC115696987 LOC115720716_LOC115696884_LOC115696986 LOC115720716_LOC115696884_LOC115697126 LOC115720716_LOC115696884_LOC115697019 LOC115720716_LOC115697762_LOC115696987 LOC115720716_LOC115697762_LOC115696986 LOC115720716_LOC115697762_LOC115697126 LOC115720716_LOC115697762_LOC115697019 LOC115720716_LOC115696987_LOC115696986 LOC115720716_LOC115696987_LOC115697126 LOC115720716_LOC115696987_LOC115697019 LOC115720716_LOC115696986_LOC115697126 LOC115720716_LOC115696986_LOC115697019 LOC115720716_LOC115697126_LOC115697019 LOC115697880_LOC115696909_LOC115696884 LOC115697880_LOC115696909_LOC115697762 LOC115697880_LOC115696909_LOC115696987 LOC115697880_LOC115696909_LOC115696986 LOC115697880_LOC115696909_LOC115697126 LOC115697880_LOC115696909_LOC115697019 LOC115697880_LOC115696884_LOC115697762 LOC115697880_LOC115696884_LOC115696987 LOC115697880_LOC115696884_LOC115696986 LOC115697880_LOC115696884_LOC115697126 LOC115697880_LOC115696884_LOC115697019 LOC115697880_LOC115697762_LOC115696987 LOC115697880_LOC115697762_LOC115696986 LOC115697880_LOC115697762_LOC115697126 LOC115697880_LOC115697762_LOC115697019 LOC115697880_LOC115696987_LOC115696986 LOC115697880_LOC115696987_LOC115697126 LOC115697880_LOC115696987_LOC115697019 LOC115697880_LOC115696986_LOC115697126 LOC115697880_LOC115696986_LOC115697019 LOC115697880_LOC115697126_LOC115697019 LOC115696909_LOC115696884_LOC115697762 LOC115696909_LOC115696884_LOC115696987 LOC115696909_LOC115696884_LOC115696986 LOC115696909_LOC115696884_LOC115697126 LOC115696909_LOC115696884_LOC115697019 LOC115696909_LOC115697762_LOC115696987 LOC115696909_LOC115697762_LOC115696986 LOC115696909_LOC115697762_LOC115697126 LOC115696909_LOC115697762_LOC115697019 LOC115696909_LOC115696987_LOC115696986 LOC115696909_LOC115696987_LOC115697126 LOC115696909_LOC115696987_LOC115697019 LOC115696909_LOC115696986_LOC115697126 LOC115696909_LOC115696986_LOC115697019 LOC115696909_LOC115697126_LOC115697019 LOC115696884_LOC115697762_LOC115696987 LOC115696884_LOC115697762_LOC115696986 LOC115696884_LOC115697762_LOC115697126 LOC115696884_LOC115697762_LOC115697019 LOC115696884_LOC115696987_LOC115696986 LOC115696884_LOC115696987_LOC115697126 LOC115696884_LOC115696987_LOC115697019 LOC115696884_LOC115696986_LOC115697126 LOC115696884_LOC115696986_LOC115697019 LOC115696884_LOC115697126_LOC115697019 LOC115697762_LOC115696987_LOC115696986 LOC115697762_LOC115696987_LOC115697126 LOC115697762_LOC115696987_LOC115697019 LOC115697762_LOC115696986_LOC115697126 LOC115697762_LOC115696986_LOC115697019 LOC115697762_LOC115697126_LOC115697019 LOC115696987_LOC115696986_LOC115697126 LOC115696987_LOC115696986_LOC115697019 LOC115696987_LOC115697126_LOC115697019 LOC115696986_LOC115697126_LOC115697019
region | VI | Normalized VI | chi2 statistics | chi2 pvalue | Jaccard |
---|---|---|---|---|---|
Loading... (need help?) |
3-gene combination was also then run, and combine the results from 1-gene, 2-gene, and 3-gene. Then sort by VI for the best and worst combination
pdvi_all=pd.concat([pdvi1, pdvi2, pdvi3])
display(pdvi_all)
The worst is LOC115720716_LOC115696909 with Normalized VI of 0.99992, and the best are LOC115718836_LOC115720716_LOC115697762 and LOC115718836_LOC115697762_LOC115697019 with NVI of 0.503647. Show the plots for these combinations
#combinations=['LOC115720716_LOC115696909', 'LOC115718836_LOC115720716_LOC115697762', 'LOC115718836_LOC115697762_LOC115697019']
# 2 projects
combinations=['LOC115720716_LOC115696884_LOC115696986','LOC115696987_LOC115696986_LOC115697019','LOC115718836_LOC115696884_LOC115697019','LOC115718836_LOC115696884']
vi_jaccard_scores=dict()
for reg in combinations:
genes=reg.split("_")
gene1range=gene2range[genes[0]]
urlloc='https://icgrc.info/api/user/variant/' + gene1range[0] + ':' + gene1range[1] + '-' + gene1range[2] + '?snpds=7ds&ref=cs10'
#reg=gene1range[0] + '_' + gene1range[1] + '_' + gene1range[2]
df_snp= read_url(urlloc,reg,requery=REQUERY_URL)
df_snp_prjn=df_snp.set_index('property',drop=False)
df_snp_prjn=df_snp_prjn.loc[:, df_snp_prjn.loc['NCBI BioProject'].isin([TYPE_PROP,'NCBI BioProject'] + prjcomb)]
df_snp_prjn=df_snp_prjn.reset_index(drop=True)
plink_extract=[]
for combs in genes:
plink_extract.append(gene2range[combs])
print(plink_extract)
vi_jaccard_scores[reg]=do_clustering(df_snp_prjn,reg+'_2prjn','cultivar_group',convert_group=convert_group,K=2,heatmap=True,plink_file=PLINKFILE,plink_extract=plink_extract,recalc=True)
[('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')]
rm: cannot remove ‘cluster_LOC115720716_LOC115696884_LOC115696986_2prjn*’: No such file or directory
group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.4914487084384396 Normalized VI=0.9897832859299888'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[38 20] [ 4 5]]
'chi2 statistic: 0.71538'
'p-value: 0.39766'
'degrees of freedom: 1'
'expected frequencies:'
array([[36.35820896, 21.64179104], [ 5.64179104, 3.35820896]])
'Chisquare statistics=0.7153817733990147 pvalue=0.3976629621283868'
'bedtools getfasta -fi /home/lmansu10/data/reference/cs10refseq.fna -bed cluster_LOC115720716_LOC115696884_LOC115696986_2prjn.btbed > cluster_LOC115720716_LOC115696884_LOC115696986_2prjn.bed.ref'
plink --bfile cluster_LOC115720716_LOC115696884_LOC115696986_2prjn --recode tab --out cluster_LOC115720716_LOC115696884_LOC115696986_2prjn_ped --allow-extra-chr
'cluster_LOC115720716_LOC115696884_LOC115696986_2prjn_ped.ped.tsv generated'
python draw_tree_matrix.py cluster_LOC115720716_LOC115696884_LOC115696986_2prjn_ped.ped.tsv cluster_LOC115720716_LOC115696884_LOC115696986_2prjn.newick
[('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]
rm: cannot remove ‘cluster_LOC115696987_LOC115696986_LOC115697019_2prjn*’: No such file or directory
group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.1055816364863778 Normalized VI=0.8873364616826944'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[48 10] [ 2 7]]
'chi2 statistic: 12.051'
'p-value: 0.00051765'
'degrees of freedom: 1'
'expected frequencies:'
array([[43.28358209, 14.71641791], [ 6.71641791, 2.28358209]])
'Chisquare statistics=12.050977574938024 pvalue=0.0005176522596520948'
'bedtools getfasta -fi /home/lmansu10/data/reference/cs10refseq.fna -bed cluster_LOC115696987_LOC115696986_LOC115697019_2prjn.btbed > cluster_LOC115696987_LOC115696986_LOC115697019_2prjn.bed.ref'
plink --bfile cluster_LOC115696987_LOC115696986_LOC115697019_2prjn --recode tab --out cluster_LOC115696987_LOC115696986_LOC115697019_2prjn_ped --allow-extra-chr
'cluster_LOC115696987_LOC115696986_LOC115697019_2prjn_ped.ped.tsv generated'
python draw_tree_matrix.py cluster_LOC115696987_LOC115696986_LOC115697019_2prjn_ped.ped.tsv cluster_LOC115696987_LOC115696986_LOC115697019_2prjn.newick
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]
rm: cannot remove ‘cluster_LOC115718836_LOC115696884_LOC115697019_2prjn*’: No such file or directory
group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.0573462366075397 Normalized VI=0.8503592514120478'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[47 11] [ 1 8]]
'chi2 statistic: 15.466'
'p-value: 8.4005e-05'
'degrees of freedom: 1'
'expected frequencies:'
array([[41.55223881, 16.44776119], [ 6.44776119, 2.55223881]])
'Chisquare statistics=15.465947330611009 pvalue=8.400512871930317e-05'
'bedtools getfasta -fi /home/lmansu10/data/reference/cs10refseq.fna -bed cluster_LOC115718836_LOC115696884_LOC115697019_2prjn.btbed > cluster_LOC115718836_LOC115696884_LOC115697019_2prjn.bed.ref'
plink --bfile cluster_LOC115718836_LOC115696884_LOC115697019_2prjn --recode tab --out cluster_LOC115718836_LOC115696884_LOC115697019_2prjn_ped --allow-extra-chr
'cluster_LOC115718836_LOC115696884_LOC115697019_2prjn_ped.ped.tsv generated'
python draw_tree_matrix.py cluster_LOC115718836_LOC115696884_LOC115697019_2prjn_ped.ped.tsv cluster_LOC115718836_LOC115696884_LOC115697019_2prjn.newick
[('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884')]
rm: cannot remove ‘cluster_LOC115718836_LOC115696884_2prjn*’: No such file or directory
group Drug group Hemp
Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.5-0). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs
'Variation of Information=1.3177836793658215 Normalized VI=0.9362915527482281'
chisquare_contingency xs=['Drug', 'Hemp'] ys=['1', '2'] [[42 16] [ 2 7]]
'chi2 statistic: 6.6221'
'p-value: 0.010072'
'degrees of freedom: 1'
'expected frequencies:'
array([[38.08955224, 19.91044776], [ 5.91044776, 3.08955224]])
'Chisquare statistics=6.6221070336044106 pvalue=0.010072060681327441'
'bedtools getfasta -fi /home/lmansu10/data/reference/cs10refseq.fna -bed cluster_LOC115718836_LOC115696884_2prjn.btbed > cluster_LOC115718836_LOC115696884_2prjn.bed.ref'
plink --bfile cluster_LOC115718836_LOC115696884_2prjn --recode tab --out cluster_LOC115718836_LOC115696884_2prjn_ped --allow-extra-chr
'cluster_LOC115718836_LOC115696884_2prjn_ped.ped.tsv generated'
python draw_tree_matrix.py cluster_LOC115718836_LOC115696884_2prjn_ped.ped.tsv cluster_LOC115718836_LOC115696884_2prjn.newick