compareSteadyNoNascent: Compare mature RNA steady state data

Description Usage Arguments Examples

View source: R/compareSteadyNoNascent-function.R

Description

This function compare exons and introns expression level matrices, from two up to an arbitrary number of samples, in order to identify genes which are oddly regluated, compared to an expected standard behaviour, from the post transcriptional point of view.

Usage

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compareSteadyNoNascent(expressionMatrices, expressionThreshold = 0.25,
  log2FCThreshold = 2)

Arguments

expressionMatrices

A list of two expression matrices, for exons and introns

expressionThreshold

Entries of exons and introns expression matrices are not take into during the analysis except for the evaluation of genes standard behaviour

log2FCThreshold

A parameter which sets how many log2 fold changes of distance from the median behaviour are imputable to noise.

Examples

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data('allcounts', package='INSPEcT')

matureCounts<-allcounts$mature

testGenes<-rownames(matureCounts$exonsCounts)

require(TxDb.Mmusculus.UCSC.mm9.knownGene)
txdb<-TxDb.Mmusculus.UCSC.mm9.knownGene

exonsDB<-reduce(exonsBy(txdb ,'gene'))
exonsDB<-exonsDB[elementNROWS(range(exonsDB))==1]
intronsDB<-psetdiff(unlist(range(exonsDB)),exonsDB)
intronsDB<-intronsDB[elementNROWS(intronsDB)>0]

exWdths<-sapply(width(exonsDB),sum)
intWdths<-sapply(width(intronsDB),sum)

exWdths<-exWdths[testGenes]
intWdths<-intWdths[testGenes]
    
totalLS<-colSums(matureCounts$
  stat[c('Assigned_Exons','Assigned_Introns'),,drop=FALSE])

expDes<-rep(c(0,1/6,1/3,1/2,1,1.5,2,4,8,12,16),3)
  
matExp_DESeq2<-quantifyExpressionsFromTrCounts(libsize=totalLS
                                            ,exonsWidths=exWdths
                                            ,intronsWidths=intWdths
                                            ,allcounts=matureCounts
                                            ,DESeq2=TRUE
                                            ,experimentalDesign=expDes)

regGenes<-compareSteadyNoNascent(expressionMatrices=matExp_DESeq2
								   ,expressionThreshold=0.25
							   ,log2FCThreshold=2.)
head(regGenes)
table(regGenes)

ste-depo/INSPEcT documentation built on July 30, 2018, 12:04 p.m.