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

In ste-depo/INSPEcT: Modeling RNA synthesis, processing and degradation with RNA-seq data

Description

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

compareSteady(inspectIds, BPPARAM = SerialParam())

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

Arguments

inspectIds	An object of calss INSPEcT with two conditions
BPPARAM	Configuration for BiocParallel parallelization. By default is set to SerialParam()

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

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 Oct. 3, 2020, 9:14 p.m.