Question: (Closed) SNP-set enrichment in GWAS analysis
0
gravatar for coleman_jonathan
6.1 years ago by
European Union
coleman_jonathan420 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 • 2.3k views
ADD COMMENTlink modified 6.1 years ago by chrchang5237.1k • written 6.1 years ago by coleman_jonathan420

Solved - see CC's answer

ADD REPLYlink modified 6 months ago by RamRS27k • written 6.1 years ago by coleman_jonathan420
3
gravatar for chrchang523
6.1 years ago by
chrchang5237.1k
United States
chrchang5237.1k wrote:

PLINK 1.07's --set-test flag may do what you need: http://pngu.mgh.harvard.edu/~purcell/plink/anal.shtml#set

ADD COMMENTlink written 6.1 years ago by chrchang5237.1k

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

ADD REPLYlink written 6.1 years ago by coleman_jonathan420
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