Test for genetic additive model using R
1
0
Entering edit mode
7 months ago
brunobsouzaa ▴ 530

Hi everyone. I'm studying two SNPs in a case/control study and one part of the analysis is to test for additive model. So the question is: Can I use logistic regression for this task or should I just build a 2x2 table and perform Fisher exact test? The data looks like this:

Outcome SNP_1 SNP_2 Gender Age
1       AA    GG    M      45
0       AC    GT    F      54
1       CC    TT    F      65

Outcome = 0 (Control); 1 (Case)

SNP_1: A = Risk

SNP_2: T = Risk

For logistic Regression, how can I format my data to fit in this kind of model? Should I just convert my genotypes to 0, 1, 2, merge both SNPs into a single column and use Outcome ~ SNP, family = binomial or there's another way to do this?

Thanks.

Additive SNP R • 269 views
ADD COMMENT
2
Entering edit mode
7 months ago

It may be worth testing an interaction term as well, such as Outcome ~ SNP_1 + SNP_2 + SNP_1:SNP_2, or the R shortcut Outcome ~ SNP_1 * SNP_2. This model would not only take into account the main effects of SNP_1 and SNP_2, but also test whether any SNP_2 SNPs influence the effect of any SNP_1 SNPs. The effectiveness of this model will somewhat depend on the sample size, since you want a good number of samples for each factor level.

ADD COMMENT
0
Entering edit mode

Thank you very much, man! Upvoted!

ADD REPLY

Login before adding your answer.

Traffic: 1865 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6