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Question: (Closed) SNP-set enrichment in GWAS analysis
0
gravatar for coleman_jonathan
3.9 years ago by
coleman_jonathan • 370
European Union
coleman_jonathan • 370 wrote:

I'm trying to see if a set of SNPs (prior candidates) are enriched in my GWAS results. This seems like something that should be do-able in PLINK, but I can't find an option... Does anyone know of a tool to do this?

 

Thanks.
gwas snp enrichment • 1.5k views
ADD COMMENT • link •
modified 3.9 years ago by chrchang523 ♦ 3.1k • written 3.9 years ago by coleman_jonathan • 370

Solved - see CC's answer

ADD REPLY • link modified 3.9 years ago • written 3.9 years ago by coleman_jonathan • 370
3
gravatar for chrchang523
3.9 years ago by
chrchang523 ♦ 3.1k
United States
chrchang523 ♦ 3.1k wrote:

PLINK 1.07's --set-test flag may do what you need: http://pngu.mgh.harvard.edu/~purcell/plink/anal.shtml#set
ADD COMMENT • link written 3.9 years ago by chrchang523 ♦ 3.1k

Thanks, Chris - don't know why I didn't spot that before!

ADD REPLY • link written 3.9 years ago by coleman_jonathan • 370
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