INSPEcT_diffsteady-class {INSPEcT} | R Documentation

## An S4 class to represent comparisons between two steady-state conditions

### Description

INSPEcT_diffsteady is a class able to store the results of the comparisons between two steady states. An object of class INSPEcT_diffsteady is created with the method "compareSteady" applied on two "INSPEcT" objects (see `compareSteady`).

### Usage

    synthesis(object)

    processing(object)

    degradation(object)

    ## S4 method for signature 'INSPEcT_diffsteady'
    show(object)

    ## S4 method for signature 'INSPEcT_diffsteady'
    synthesis(object)

    ## S4 method for signature 'INSPEcT_diffsteady'
    processing(object)

    ## S4 method for signature 'INSPEcT_diffsteady'
    degradation(object)

    ## S4 method for signature 'INSPEcT_diffsteady'
    featureNames(object)

### Arguments

`object` | An object of class INSPEcT_model

### Details

Methods associated to the class INSPEcT_diffsteady are:

- synthesis: Accessor to the synthesis rates and their comparisons.

- degradation: Accessor to the degradation rates and their comparisons.

- processing: Accessor to the processing rates and their comparisons.

- plotMA: visualization fuction for rates comparisons, see `plotMA`

### Value

Method show for objects of class INSPEcT_model returns the number of the genes that have been modeled

### Slots

`synthesis`

  A data.frame which contains both input data and comparisons results regarding synthesis rates

`degradation`

  A data.frame which contains both input data and comparisons results regarding degradation rates

`processing`

  A data.frame which contains both input data and comparisons results regarding processing rates

`modeling_res`

  A data.frame which contains modeling results

### 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)])
      head(synthesis(diffrates))
    }
    if( Sys.info()["sysname"] != "Windows" ) {
      head(processing(diffrates))
    }
    if( Sys.info()["sysname"] != "Windows" ) {
      head(degradation(diffrates))
    }
    if( Sys.info()["sysname"] != "Windows" ) {
      featureNames(diffrates)
    }

[Package INSPEcT version 1.22.0 Index]