Any suggestions on tool/methods for gene based analysis?
Data: I have all the GWAS data for case-control samples n=100K:
- genotyped GWAS (~600K SNPs, maybe useful for LD)
- imputed GWAS (IMPUTE Phase3, more SNPs)
- meta summary data based on multiple imputed GWAS data (IMPUTE2 Phase3, maybe more power, p-values)
Aim: X, Y, and Z genes are significant when all the SNPs within the gene boundaries (with flanks?) p-values are collapsed.
I remember testing VEGAS (5-6 years ago), thought now maybe new better tools are around.
Side question, what is the suggested boundary flanks for genes, 10K, 20K? These boundaries seems silly when genes are tiny.
I would prefer to stay in
R world, but happy to switch if the tool is good enough.
Let me know if you need more info.