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: 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