chr1swallace/coloc

Results from coloc.abf

Duhh56 opened this issue · 3 comments

Duhh56 commented

Hi,

Thanks for developing the package, I am using coloc.abf and have run the following function:

coloc_abf_AL <- coloc.abf(dataset1 = list(beta=coloc_df$BETA, varbeta=coloc_df$Varbeta, N=1597, type="quant", MAF=coloc_df$maf, pvalues=coloc_df$P, snp=coloc_df$ID), dataset2 = list(beta=coloc_df$slope, varbeta=coloc_df$eQTL_Varbeta, N=605, type="quant", MAF=coloc_df$maf, pvalues=coloc_df$pval_nominal, snp=coloc_df$ID))

I get the result

> print(coloc_abf_AL$summary)
       nsnps    PP.H0.abf    PP.H1.abf    PP.H2.abf    PP.H3.abf    PP.H4.abf 
3.830000e+03 6.043220e-07 8.186484e-07 4.134895e-01 5.601097e-01 2.639932e-02

I am not sure what the result means? Is this saying all my SNPs (3830) have posterior probability of 0%? Therefore, no co-localization of GWAS signals and eQTLs was found?

tss0222 commented

I also would like to ask how to interpret the result when PP.H4.abf is less than 0.95 but SNP.PP.H4 is larger than 0.95

chr1swallace commented
chr1swallace commented