plotMA {INSPEcT} | R Documentation

## MA-plot from base means and log fold changes

### 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)
    }

[Package INSPEcT version 1.20.0 Index]