Test For Association While Allowing For Interaction And Test For Interaction

Question

[Liyf]

Epistasis, when using in GWAS data, has some difficulties especially the large data size. So many methods were developed to select a set of snps while others do the detection of pairs discovery. I read some reviews which said, there are test for interaction and test for association while allowing for interaction, just as they said, I wonder whether the test for association while allowing for interaction is just the method that select a set of snps?

Answer 1

[Fayue1015]

I would refer you to a paper Detecting two-locus associations allowing for interactions in genome-wide association studies. Bioinformatics. X. Wan, C. Yang, Q. Yang, H. Xue, N. Tang and W. Yu. * joint first author.

which can clear your doubt in mind.

[Liyf]

Thanks, I will.

Answer 2

[David Quigley]

Testing for association while allowing for interaction most likely means that the model they are fitting has terms for each individual SNP being tested as well as a term for the interaction of those SNPs. A test for association not allowing for interaction would contain additive terms for each individual SNP but not a term for the non-additive combination of the effect of the SNPs. If that doesn't make it clear, I suggest you look for an introduction to linear regression.

[Liyf]

Clear, thank you. I got it :)

[David Quigley]

Glad to help. If you consider this (or any other question you ask) to be answered, please mark the answer with the check mark on the left side of the answer.