Pathway analysis using rare-variant SKAT-O summary statistics

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2.2 years 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

etc

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: https://github.com/yaowuliu/ACAT/blob/master/doc/ACAT_manual.pdf and was wondering if anyone had any experience with similar tools?

Many thanks for your help

variant rare pathway analysis R • 680 views

ADD COMMENT • link updated 2.2 years ago by LChart 4.7k • written 2.2 years ago by tacrolimus ▴ 140

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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.

ADD REPLY • link 2.2 years ago by LChart 4.7k

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