[GenABEL-dev] No COVAR variable in output when using --robust with the --mmscore option

[Bragg-Gresham, Jennifer]

Hello,

I am trying to use the palinear software to run GWAS with genotype*covariate interactions and I have family pedigree to account for. I have the software running with the -mmscore function and with the -robust function, but I am not getting the COVAR_SNP_INT variable in my output files. I can get them if I remove the -mmscore function, but that is not helpful, obviously. I am wondering if this a bug in the program or if there is something else I need to do.

Here is my command line:

runon $bin/palinear --pheno $pheno/${trt}1a2_${who}.txt --dose $pheno/doses/$i.mldose.gz  --info .temp.$i.mlinfo --interaction=1 --robust --mmscore $pheno/InvVarCov_matrix_${trt}1a2_${who} --out $pheno/MODEL2/$who.$trt.$i > $pheno.$who.$trt.$i.log

Thank you for any assistance you can provide,

Jennifer

--
Jennifer L. Bragg-Gresham, MS
Center for Statistical Genetics
Department of Biostatistics
University of Michigan
1415 Washington Heights
Ann Arbor, MI 48109-2029

Phone: (734) 763-2161
Fax: (734) 615-8322

Office: 4622 SPH I
E-mail: jennb at umich.edu<mailto:jennb at umich.edu>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/genabel-devel/attachments/20110609/d8eab52e/attachment.htm>