Question: GWAS on dosage data - interaction
1
gravatar for Abdel
5.2 years ago by
Abdel350
Amsterdam
Abdel350 wrote:

Is there a software package for GWASs that can include an interaction effect (SNP x predictor) in the regression using dosage data?

snp interaction gwas • 3.1k views
ADD COMMENTlink modified 6 days ago by joeyinjie0 • written 5.2 years ago by Abdel350
3
gravatar for coleman_jonathan
5.2 years ago by
European Union
coleman_jonathan420 wrote:

Can you use PLINK2: https://www.cog-genomics.org/plink2/assoc#linear ?

 

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?

ADD COMMENTlink written 5.2 years ago by coleman_jonathan420

My best-guess genotypes unfortunately don't work as well as my dosage data for some reason...

I'll check if plink2 can handle dosage data in this way, thanks!

ADD REPLYlink written 5.2 years ago by Abdel350
1

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

ADD REPLYlink modified 5.2 years ago • written 5.2 years ago by chrchang5235.5k

snptest does not handle SNP interactions.

ADD REPLYlink written 4.6 years ago by Tafelplankje120

that version does not handle dosage data in combination with interaction...

ADD REPLYlink modified 4.6 years ago • written 4.6 years ago by Tafelplankje120
1
gravatar for Devon Ryan
5.2 years ago by
Devon Ryan91k
Freiburg, Germany
Devon Ryan91k wrote:

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.

ADD COMMENTlink written 5.2 years ago by Devon Ryan91k

It's a linear regression. And Plink unfortunately can't do that...

ADD REPLYlink modified 5.2 years ago • written 5.2 years ago by Abdel350

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.

ADD REPLYlink written 5.2 years ago by Devon Ryan91k

Large datasets and R are a pain in the ass...

ADD REPLYlink written 4.6 years ago by Tafelplankje120

Depends on how much memory you have, but yes, it can become problematic.

ADD REPLYlink written 4.6 years ago by Devon Ryan91k
0
gravatar for Tafelplankje
4.5 years ago by
Tafelplankje120
Netherlands
Tafelplankje120 wrote:

you could also use quicktest http://toby.freeshell.org/software/quicktest.shtml

ADD COMMENTlink written 4.5 years ago by Tafelplankje120
0
gravatar for joeyinjie
6 days ago by
joeyinjie0
joeyinjie0 wrote:

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!

ADD COMMENTlink written 6 days ago by joeyinjie0

plink 2.0 —glm handles dosage data and interactions.

ADD REPLYlink written 6 days ago by chrchang5235.5k

Thanks a lot! I’ll try it.

ADD REPLYlink written 6 days ago by joeyinjie0
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