compareSteady: Generate an object of class INSPEcT_diffsteady from an object...
In INSPEcT: Modeling RNA synthesis, processing and degradation with RNA-seq data

Description Usage Arguments Value Examples

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.

compareSteady(inspectIds, BPPARAM = SerialParam())

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

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

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)

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)])
}