Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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.

Latest Articles

Collapse

  • seqadmin
    Strategies for Sequencing Challenging Samples
    by seqadmin


    Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
    03-22-2024, 06:39 AM
  • seqadmin
    Techniques and Challenges in Conservation Genomics
    by seqadmin



    The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

    Avian Conservation
    Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
    03-08-2024, 10:41 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 06:37 PM
0 responses
8 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 06:07 PM
0 responses
8 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
49 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-21-2024, 07:32 AM
0 responses
66 views
0 likes
Last Post seqadmin  
Working...
X