plotMA: MA-plot from base means and log fold changes

Description Usage Arguments Details See Also Examples

Description

Visualize the comparison between the rates calculated from two different INSPEcT objects profiled in steady-state conditions.

Usage

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## S4 method for signature 'INSPEcT_diffsteady'
plotMA(object, ...)

Arguments

object

An object of calss INSPEcT_diffsteady

...

Additional parameters, see Details section

Details

Possible arguments to "plotMA":

See Also

http://en.wikipedia.org/wiki/MA_plot

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)])
 
  plotMA(diffrates, padj=.01)
}

ste-depo/INSPEcT documentation built on Oct. 3, 2020, 9:14 p.m.