getGeneExpression: Calculate gene expression or relative within gene expression

In BitSeq: Transcript expression inference and differential expression analysis for RNA-seq data

Description

Calculate either gene expression or relative within gene expression using transcript expression samples and transcript information file.

Usage

getGeneExpression(sampleFile, outFile=NULL, trInfo=NULL, trInfoFile=NULL,
      pretend=FALSE)
getWithinGeneExpression(sampleFile, outFile=NULL, trInfo=NULL, trInfoFile=NULL,
      pretend=FALSE, keepOrder=FALSE)

Arguments

sampleFile	File containing the transcript expression samples.
outFile	Name of the output file. If not used, function uses temporary file.
trInfo	DataFrame containing transcript information. Either trInfo or trInfoFile argument has to be provided. Otherwise function tries file with same name as sampleFile and extension tr.
trInfoFile	Transcript information file. Either trInfo or trInfoFile argument has to be provided. Otherwise function tries file with same name as sampleFile and extension tr.
pretend	Do not execute, only print out command line calls for the C++ version of the program.
keepOrder	If TRUE then transcripts will always keep same order, otherwise transcripts might be grouped by genes in the output. (The order is always same if transcripts are grouped by genes.)

Details

The getGeneExpression function takes samples of transcript expression and produces file with expression of genes by adding up transcript expression.

The getWithinGeneExpression function takes samples of transcript expression and produces file with relative within gene expression samples for each transcript.

Both function need valid transcript information which contains gene transcript mapping. This can be provided either via DataFrame trInfo or file named trInfoFile.

In case of a file, it should be formatted in following manner. The first line should contain "# M <numberOfTranscripts>" and the following numberOfTranscripts lines have to contain "<geneName> <transcriptName> <transcriptLength>". Example is provided in extdata/ensSelect1.tr. Please note that the transcript information file automatically generated from alignment files are not sufficient because SAM/BAM files do not include gene names. We hope to provide more convenient way in future versions of BitSeq.

Value

Name of file containing the new expression samples.

Author(s)

Peter Glaus

See Also

getExpression, tri.load, tri.file.setGeneNames, tri.file.hasGeneNames

Examples

setwd(system.file("extdata",package="BitSeq"))
## use transcript information as object
trinfo <- tri.load("ensSelect1.tr")
## gene expression
getGeneExpression("data-c0b1.rpkm", "data-c0b1-GE.rpkm", trInfo=trinfo)
gExpSamples <- loadSamples("data-c0b1-GE.rpkm")
gExpMeans <- rowMeans(as.data.frame(gExpSamples))
gExpMeans

## within gene expression
wgeFN <- getWithinGeneExpression("data-c0b1.rpkm", trInfoFile="ensSelect1.tr")
wgExpSamples <- loadSamples(wgeFN)
wgExpMeans <- rowMeans(as.data.frame(wgExpSamples))
head(wgExpMeans)

BitSeq documentation built on Nov. 8, 2020, 5:25 p.m.