cov_SNP_int_SNP_covariate & mmscore

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dadaru
Posts: 2
Joined: Mon Sep 29, 2014 1:21 pm

cov_SNP_int_SNP_covariate & mmscore

Postby dadaru » Mon Sep 29, 2014 1:52 pm

Hi,

I'm trying to use palinear to perform an association analysis considering the interaction between a covariate and the SNPs, in presence of relatedness between the individuals. The options that I'm using are --mmscore --interaction --robust.
In the output file is not present the column "cov_SNP_int_SNP_covariate". How can I obtain it?
I'm using the ProbABEL v.0.4.3.

Thanks,
Daniela

lckarssen
Site Admin
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Posts: 321
Joined: Tue Jan 04, 2011 3:04 pm
Location: Utrecht, The Netherlands

Re: cov_SNP_int_SNP_covariate & mmscore

Postby lckarssen » Fri Mar 06, 2015 5:24 pm

Sorry for the late reply.

I think your question is a duplicate of the one in this post: viewtopic.php?f=10&t=830&p=1662 There, a suggestion is made to take a look at MixABEL. That may be a good option for you as well.

About ProbABEL: it looks like this is a bug. I've filed a bug report about it in our tracker (Bug #6045).
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Lennart Karssen
PolyOmica
The Netherlands
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dadaru
Posts: 2
Joined: Mon Sep 29, 2014 1:21 pm

Re: cov_SNP_int_SNP_covariate & mmscore

Postby dadaru » Thu Sep 15, 2016 9:57 am

Dear Lennart,

as you suggested me, I've tried to use MixABEL to perform GxE analysis in presence of relatedness but, as reported also by other users, I have difficulties in installing the version 0.0-9 that is downloadable from the GenABEL site.

In a recent paper (http://www.nature.com/articles/ncomms11008) I have read that MixABEL v0.1-1 has been used by Framingham group to perform the GWAS, and I have also read your recent pubblication (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4916982/) in which you describe the MixABEL v0.1-3, released in 2015.

Where are these updated MixABEL versions available for download? Have you planned to put an updated version on the GenABEL website?
Alternatively, have you planned to solve the bug of ProbABEL (https://github.com/GenABEL-Project/ProbABEL/issues/2) to make it output the cov_SNP_int_SNP_covariate column when using --mmscore and --interaction?

Best,
Daniela


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