Pathway analysis using rare-variant SKAT-O summary statistics
Entering edit mode
10 months ago
tacrolimus ▴ 140

Dear Biostars,

I have summary stats from a SAIGE-GENE analysis of a case-control cohort. This is a collapsing rare variant test and the output has a heading like this:

GENE      Pvalue
ABC         0.093 
LOL2       1.123e-78
KJD         0.192


I would like to do a gene-set analysis looking at the enrichment of pathways and was wondering if there was a method that used summary stats like this only? I have the individual markers, their AFs,BETA's, Pvalues etc but I would rather not format them into something like MAGMA if I can avoid the extra effort.

I have found this: and was wondering if anyone had any experience with similar tools?

Many thanks for your help

variant rare pathway analysis R • 408 views
Entering edit mode

You can use fgsea with the p-value ranked list of genes, and a simple hypergeometric test using a p-value cutoff. Tons of R packages are out there which implement pathway enrichment analysis; my personal choice is piano.


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