Hello,
I am working on case-control study and would like to understand how to calculate and interpret the hom/het ratio distribution of the minor allele. A test data generated from plink --model is as follows
What I assume is that snp2 shows the best p value in the recessive model so I would assume there are more homozygous alleles than expected. And snp1 shows a stronger dominant effect so there could be more heterozygous alleles. But how can I know if the distribution of aa/aA/AA is correct and this data can be analysed further?
Thank you..
I am working on case-control study and would like to understand how to calculate and interpret the hom/het ratio distribution of the minor allele. A test data generated from plink --model is as follows
Code:
CHR SNP A1 A2 TEST AFF UNAFF P 1 snp1 A1 A2 GENO 0/25/1465 0/35/1010 0.008 1 snp1 A1 A2 TREND 25/2955 35/2060 0.005 1 snp1 A1 A2 ALLELIC 25/2955 35/2060 0.01 1 snp1 A1 A2 DOM 25/1465 35/1010 0.009 1 snp1 A1 A2 REC 0/1490 0/1050 1 2 snp2 A1 A2 GENO 75/230/1250 9/140/890 1.6e-05 2 snp2 A1 A2 TREND 380/2730 158/1925 2.6e-03 2 snp2 A1 A2 ALLELIC 380/2730 158/1925 1.0e-06 2 snp2 A1 A2 DOM 305/1250 149/890 0.0004 2 snp2 A1 A2 REC 75/1480 9/1035 2.2e-2
Thank you..