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Old 11-25-2013, 06:40 AM   #1
nans_bn
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Location: United Kingdom

Join Date: Mar 2011
Posts: 12
Default het:hom distribution in case-control study

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

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
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..

Last edited by nans_bn; 11-26-2013 at 02:24 AM.
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