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Question: (Closed) SNP-set enrichment in GWAS analysis
0
gravatar for coleman_jonathan
6.7 years ago by
coleman_jonathan • 440
European Union
coleman_jonathan • 440 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 • 2.4k views
ADD COMMENT • link •
modified 6.7 years ago by chrchang523 ♦ 7.6k • written 6.7 years ago by coleman_jonathan • 440

Solved - see CC's answer

ADD REPLY • link modified 12 months ago by _r_am ♦ 32k • written 6.7 years ago by coleman_jonathan • 440
3
gravatar for chrchang523
6.7 years ago by
chrchang523 ♦ 7.6k
United States
chrchang523 ♦ 7.6k 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 6.7 years ago by chrchang523 ♦ 7.6k

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

ADD REPLY • link written 6.7 years ago by coleman_jonathan • 440
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