R help - Feb 2011 - GWAF package: lme.batch.imputed(): object 'kmat' not found

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]]

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 <moonja at ohsu.edu>
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]]
>
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