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

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

Description

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

Usage

## 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":

• "rate" - A character, which represent the rate to be visualized, either "synthesis", "processing" or "degradation". By default, "synthesis" is chosen.

• "padj" - A numeric, The p-adjusted threshold for significance. Genes with p-adjusted lower than the threshold will be depicted as orange triangles. By default set to -Inf, meaning that no genes will be highlighted.

• "xlim" - A numeric vector of length 2, limits of x-axis, by default the range of the data.

• "xlab" - A character, the label of x-axis, by default "log2 geometric mean"

• "ylim" - A numeric vector of length 2, limits of y-axis, by default the range of the data.

• "ylab" - A character, the label of y-axis, by default "log2 fold change"

• "main" - A character, the title of the plot, by default the name of the visualized rate.

See Also

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

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

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