Entering edit mode
7.2 years ago
dizue
▴
30
I am trying to do a mQTL enrichment analysis using permutation method. However, I encountered some problem here.
I understand that I have to select 'control' SNPs that match the MAF and LD with mQTL. So I selected those from the 1000 Genomes pilot 1 data, with MAF r2>0.8 and LD around 10kb of the mQTL.
Then I plotted the MAF distribution of the entire control SNPs and the MAF distribution of the mQTL
The problem is there aren't many control SNPs with small MAF in the control set. When I tried to do the permutation, I have to randomly choose 3000 SNPs out of the 3500 SNPs. Is the permutation still valid?
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