* collab: (34 commits)
revert change to IlluminaPreprocessCN
fix bug in isValidCdfName
print warning when all features in a batch of probes are flagged, but allow processing to continue
add utility cleancdfnames
Add validCdfNames.Rd
export validCdfNames
imputeGender fix when chromosome Y not available
Use splitIndicesByLength(index, ocSamples/getDoParWorkers())
Can not allocate vector of size XG with genotype.Illumina. Use splitIndicesByNode() only if the length of the list is greater than the split from splitIndicesByLength(). Otherwise, split by length using ocSamples()
update .gitignore
Add make.unique for sampleSheet$Sample_ID in readIdatFiles
bug in description
ensure sample ids stored in samplesheet are unique when constructing cnSet object
update oligoClasses dependency
update unit test for genotype.Illumina
revert change in constructInf call from genotype.Illumina
Update genotype.Rd
edit ACN function
1.15.6 use make.unique(basename(arrayNames)) to allow processing of Illumina samples with duplicated barcodes
check that sample identifies are unique in crlmm function
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git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@67435 bc3139a8-67e5-0310-9ffc-ced21a209358
Rob Scharp authored on 08/07/2012 19:00:03
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+\name{validCdfNames}
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+\alias{validCdfNames}
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+ |
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+\title{ Supported annotation packages for crlmm genotyping}
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+\description{
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+Supported annotation packages for crlmm genotyping |
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+} |
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+\usage{
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+validCdfNames() |
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+} |
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+\details{
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+ List of available annotation packages |
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+} |
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+\value{
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+ character vector |
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+} |
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+ |
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+\author{
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+R.Scharpf |
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+} |
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+ |
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+ |
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+\examples{
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+validCdfNames() |
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+} |
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+\keyword{manip}
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\ No newline at end of file |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@45126 bc3139a8-67e5-0310-9ffc-ced21a209358
Rob Scharp authored on 10/03/2010 01:27:04
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-\name{validCdfNames}
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-\alias{validCdfNames}
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-\title{
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- Valid R package for annotating crlmm or illumina platforms |
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-} |
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-\description{
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- Returns a list of the platforms that are currently supported. |
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-} |
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-\details{
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- |
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-} |
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-\value{
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- Vector of currently supported platforms. |
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-} |
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-\references{
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- } |
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-\author{
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- R. Scharpf |
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-} |
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- |
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- |
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-\examples{
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- validCdfNames() |
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-} |
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-\keyword{manip}
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- |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@45083 bc3139a8-67e5-0310-9ffc-ced21a209358
Rob Scharp authored on 08/03/2010 04:46:55
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+\name{validCdfNames}
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+\alias{validCdfNames}
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+\title{
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+ Valid R package for annotating crlmm or illumina platforms |
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+} |
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+\description{
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+ Returns a list of the platforms that are currently supported. |
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+} |
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+\details{
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+ |
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+} |
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+\value{
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+ Vector of currently supported platforms. |
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+} |
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+\references{
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+ } |
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+\author{
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+ R. Scharpf |
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+} |
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+ |
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+ |
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+\examples{
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+ validCdfNames() |
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+} |
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+\keyword{manip}
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+ |