From 0228e728e17bffe6603c365ca950778bcfa59387 Mon Sep 17 00:00:00 2001 From: hjulienn <hanna.julienne@pasteur.fr> Date: Wed, 30 Nov 2022 14:24:59 +0100 Subject: [PATCH] correction in doc --- doc/source/index.rst | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/doc/source/index.rst b/doc/source/index.rst index 85f30e7..a13ff11 100644 --- a/doc/source/index.rst +++ b/doc/source/index.rst @@ -10,6 +10,8 @@ Welcome to jass_preprocessing's documentation! :maxdepth: 2 :caption: Contents: + index + What is jass preprocessing ? ============================ Jass preprocessing is a tool that takes in input @@ -97,11 +99,15 @@ 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! +Some fields are optional like the imputation_quality. If not used they can be filled with na. + +.. csv-table:: GWAS information table + :header-rows: 1 + + "filename","consortia","outcome","fullName","type","Nsample","Ncase","Ncontrol","Nsnp","snpid","a1","a2","freq","pval","n","z","OR","se","code","imp","ncas","ncont","imputation_quality","index_type" + "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","rs-number" + - :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: -- GitLab