compareSteady {INSPEcT} | R Documentation

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

### 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 = 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

    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)])
    }

[Package INSPEcT version 1.12.2 Index]