Commit 3a03bac4 authored by Hanna  JULIENNE's avatar Hanna JULIENNE
Browse files

fix filer on imputation quality

parent b0380f32
Pipeline #44528 passed with stages
in 1 minute and 22 seconds
......@@ -97,11 +97,11 @@ Input
Note that the combination of Consortium and outcome must be unique because it will be used as an index in the cleaning process.
Here is an example of descriptor field, the field irrelevant (for example odd ratio for continuous trait) for the study must be filled with na.
Some fields are optional like the imputation_quality. If not used they can be filled with na.
.. csv-table:: GWAS information table!
:header: "filename","consortia","outcome","fullName","type","Nsample","Ncase","Ncontrol","Nsnp","snpid","a1","a2","freq","pval","n","z","OR","se","code","imp","ncas","ncont"
"GIANT_HEIGHT_Wood_et_al.txt","GIANT","HEIGHT","Height","Anthropometry",253288, na, na, 2550858, "MarkerName", "Allele1", "Allele2", "Freq.Allele1.HapMapCEU","p","N","b",na,"SE",na,na,na,na
:header: "filename","consortia","outcome","fullName","type","Nsample","Ncase","Ncontrol","Nsnp","snpid","a1","a2","freq","pval","n","z","OR","se","code","imp","ncas","ncont","imputation_quality"
"GIANT_HEIGHT_Wood_et_al.txt","GIANT","HEIGHT","Height","Anthropometry",253288, na, na, 2550858, "MarkerName", "Allele1", "Allele2", "Freq.Allele1.HapMapCEU","p","N","b",na,"SE",na,na,na,na, "imputationInfo"
Command line usage example:
......
......@@ -169,7 +169,7 @@ def read_gwas( gwas_internal_link, column_map, imputation_treshold=None):
print(fullGWAS.head())
if imputation_treshold:
fullGWAS = fullGWAS.loc[fullName.imputation_quality > imputation_treshold]
fullGWAS = fullGWAS.loc[fullGWAS.imputation_quality > imputation_treshold]
fullGWAS = fullGWAS[~fullGWAS.index.duplicated(keep='first')]
#fullGWAS = convert_missing_values(fullGWAS)
......
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