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  • 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, 02:24 AM.

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