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Stahl-Lab-MSSM / coloc2

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File format #3

Open xtmgah opened 5 years ago

xtmgah commented 5 years ago

Hello, Do you have any information about the file format for GWAS summary and eQTL summary statical data? thanks

kumimesy commented 5 years ago

Hi, I also want to know the file format. When I try to use "formatColoc" function, I got the following error message.

Error in setnames(ans, col.names) : Passed a vector of type 'NULL'. Needs to be type 'character'.

Thanks.

adobbyn commented 5 years ago

Hi both, sorry for the delayed response. The documentation for coloc should largely be applicable to coloc2 as well, including file formats. In order to run the analysis, summary statistics should include either betas and standard errors (preferred) or p-values. Below are toy examples of GWAS and eQTL file formats:

GWAS:

snp chr pos A1 A2 N beta StdErr Zscore INFO
rs575272151 1 11008 G C 10000 0.00493700391030691 0.0095217414730759 0.518498 0.110114

eQTL:

variant_id ProbeID maf beta se chr pos A1 A2 snp
1_100000012_G_T ENSG00000122477 0.2 -0.01 0.02 1 100000012 G T rs10875231
kumimesy commented 5 years ago

Hi adobbyn, thanks for your kind reply. I wonder if I can use z-score and p-value in eQTL data instead of beta and se. Actually there are no beta/SE in my eQTL data. Thanks.