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  • Committer: Package Import Robot
  • Author(s): Andreas Tille
  • Date: 2013-12-28 17:17:25 UTC
  • mfrom: (1.1.2)
  • Revision ID: package-import@ubuntu.com-20131228171725-polmzo8go4m371c6
Tags: 2.4.1-1
* New upstream version
* debian/rules: Remove useless creation of ${R-Depends}
* debian/control: Versioned Build-Depends: r-base-dev (>= 3.0)
* debian/README.test: add hint how to test the package

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man/countMatrix.Rd
 
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\name{countMatrix}
 
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\alias{countMatrix}
 
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\alias{countMatrix,CuffData-method}
 
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\alias{countMatrix,CuffFeatureSet-method}
 
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\alias{repCountMatrix}
 
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\alias{repCountMatrix,CuffData-method}
 
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\alias{repCountMatrix,CuffFeatureSet-method}
 
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%- Also NEED an '\alias' for EACH other topic documented here.
 
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\title{
 
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countMatrix
 
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}
 
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\description{
 
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Retrieve count values as gene by condition matrix
 
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}
 
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\usage{
 
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\S4method{countMatrix}{CuffData}(object,fullnames=FALSE,sampleIdList)
 
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\S4method{repCountMatrix}{CuffData}(object,fullnames=FALSE,repIdList)
 
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}
 
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\arguments{
 
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  \item{object}{
 
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An object of class ('CuffData','CuffFeatureSet','CuffGeneSet','CuffGene',or 'CuffFeature')
 
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}
 
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  \item{fullnames}{
 
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A logical value whether or not to concatenate gene_short_name and tracking_id values (easier to read labels)
 
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}
 
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  \item{sampleIdList}{
 
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A vector of sample names to subset the resulting matrix.
 
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}
 
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  \item{repIdList}{
 
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A vector of replicate names to subset the resulting replicate matrix.
 
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}
 
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}
 
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\details{
 
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None.
 
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}
 
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\value{
 
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A feature x condition matrix of count values.
 
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}
 
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\references{
 
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None.
 
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}
 
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\author{
 
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Loyal A. Goff
 
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}
 
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\note{
 
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None
 
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}
 
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\examples{
 
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        data(sampleData)
 
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        countMatrix(sampleGeneSet)
 
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        repCountMatrix(sampleGeneSet)
 
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}