GWAF uses the kinship package. The documentation is pretty good for it, and I've used it successfully. It may be helpful to get that working before trying automate some tasks using GWAF.
On Fri, Feb 4, 2011 at 2:20 PM, Jim Moon <[email protected]> wrote: > Hello, All, > > GWAF 1.2 > R.Version() is below. > > system(lme.batch.imputed( > phenfile = 'phenfile.csv', > genfile = 'CARe_imputed_release.0.fhsR.gz', > pedfile='pedfile.csv', > phen='phen1', > covar=c('covar1','covar2'), > kinmat='imputed_fhs.kinship.RData', > outfile='imputed.FHS.IBC.GWAF.LME.output.0.txt' > )) > > Gives the error messages: > > Error in coxme.varcheck(ncluster, varlist, n, gvars, groups, sparse, rescale, > : > object 'kmat' not found > Error in lme.cov.out$theta : $ operator is invalid for atomic vectors > > Might anyone know why? > > Thank you for your time! > > Jim > > --------------------------------------------------- >> R.Version() > $platform > [1] "x86_64-apple-darwin9.6.0" > > $arch > [1] "x86_64" > > $os > [1] "darwin9.6.0" > > $system > [1] "x86_64, darwin9.6.0" > > $status > [1] "" > > $major > [1] "2" > > $minor > [1] "12.1" > > $year > [1] "2010" > > $month > [1] "12" > > $day > [1] "16" > > $`svn rev` > [1] "53855" > > $language > [1] "R" > > $version.string > [1] "R version 2.12.1 (2010-12-16)" > > [[alternative HTML version deleted]] > > ______________________________________________ > [email protected] mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > ______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
