Is there a software package for GWASs that can include an interaction effect (SNP x predictor) in the regression using dosage data?
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written
by
Abdel
4 answers
Can you use PLINK2?
That provides an interaction term for the linear regression... In terms of the dosage data, do you have to use the probabilistic data, or would best-guess hard-calling work?
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written
by
coleman_jonathan
PLINK 2.0 will have proper support for dosage data, but 1.9 cannot since it is limited by the PLINK 1 file format.
SNPTEST may be your best bet for this: https://mathgen.stats.ox.ac.uk/genetics_software/snptest/snptest.html
snptest does not handle SNP interactions.
that version does not handle dosage data in combination with interaction...
Assuming you're using a logistic regression for the underlying statistic, then you could do that in R easily enough. I'd also be very surprised if plink can't do that too.
I'm surprised that plink won't handle that, that would seem to be a useful feature. Either way, you can just do it in R, which will handle pretty much any model you want.
Large datasets and R are a pain in the ass...
Depends on how much memory you have, but yes, it can become problematic.
I have the same problem recently. Just want to ask if PLINK2.0 handled your problem that - - interaction doesn’t run with dosage data. Thanks!
plink 2.0 —glm handles dosage data and interactions.
Thanks a lot! I’ll try it.
you could also use quicktest http://toby.freeshell.org/software/quicktest.shtml
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