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Question: (Closed) SNP-set enrichment in GWAS analysis
0
gravatar for coleman_jonathan
4.7 years ago by
coleman_jonathan • 400
European Union
coleman_jonathan • 400 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 • 1.8k views
ADD COMMENT • link •
modified 4.7 years ago by chrchang523 ♦ 4.3k • written 4.7 years ago by coleman_jonathan • 400

Solved - see CC's answer

ADD REPLY • link modified 4.7 years ago • written 4.7 years ago by coleman_jonathan • 400
3
gravatar for chrchang523
4.7 years ago by
chrchang523 ♦ 4.3k
United States
chrchang523 ♦ 4.3k 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 4.7 years ago by chrchang523 ♦ 4.3k

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

ADD REPLY • link written 4.7 years ago by coleman_jonathan • 400
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