compareSteady: Generate an object of class INSPEcT_diffsteady from an object...

Description Usage Arguments Value Examples

Description

Generate an object of class INSPEcT_diffsteady from an object of class INSPEcT

This method compares two object of class INSPEcT in order to identify differential usage of synthesis, processing or degradation rates in two different steady-state conditions. The two INSPEcT objects must have been profiled with replicates in order to provide a statistical significance to the differences between their rates.

Usage

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compareSteady(inspectIds, BPPARAM = bpparam())

## S4 method for signature 'INSPEcT'
compareSteady(inspectIds, BPPARAM = bpparam())

Arguments

inspectIds

An object of calss INSPEcT with two conditions

BPPARAM

Configuration for BiocParallel parallelization. By default is set to bpparam()

Value

An object of class INSPEcT_diffsteady which contains both the absolute quantification of the rates as well as the comparison with the statistical significance associated for each gene and rate. (See INSPEcT_diffsteady-class)

Examples

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if( Sys.info()["sysname"] != "Windows" ) {
  data('allcounts', package='INSPEcT')
  data('featureWidths', package='INSPEcT')
  data('libsizes', package='INSPEcT')
  
  nascentCounts<-allcounts$nascent
  matureCounts<-allcounts$mature
  conditions<-letters[1:11]
  expDes<-rep(conditions,3)
  tL<-1/6
  
  nasExp_DESeq2<-quantifyExpressionsFromTrCounts(
        allcounts=nascentCounts
        ,libsize=nascentLS
        ,exonsWidths=exWdths
        ,intronsWidths=intWdths
        ,experimentalDesign=expDes)
  
  matExp_DESeq2<-quantifyExpressionsFromTrCounts(
        allcounts=matureCounts
        ,libsize=totalLS
        ,exonsWidths=exWdths
        ,intronsWidths=intWdths
        ,experimentalDesign=expDes)
 
  nasFullObj <- newINSPEcT(
        tpts=conditions
        ,labeling_time=tL
        ,nascentExpressions=nasExp_DESeq2
        ,matureExpressions=matExp_DESeq2)
  
  diffrates = compareSteady(nasFullObj[,c(1,11)])
}

ste-depo/INSPEcT documentation built on Jan. 21, 2019, 5:46 a.m.