duprateExpDensPlot: Duplication rate ~ total read count plot
In dupRadar: Assessment of duplication rates in RNA-Seq datasets

Description Usage Arguments Details Value Examples

duprateExpDensPlot Duplication rate ~ total read count plot

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duprateExpDensPlot(DupMat, pal = c("cyan", "blue", "green", "yellow", "red"),
  tNoAlternative = TRUE, tRPKM = TRUE, tRPKMval = 0.5, tFit = TRUE,
  addLegend = TRUE, ...)

`DupMat`	The duplication matrix calculated by `analyzeDuprates`
`pal`	The color palette to use to display the density
`tNoAlternative`	Display threshold of 1000 reads per kilobase
`tRPKM`	Display threshold at a given RPKM level
`tRPKMval`	The given RPKM level
`tFit`	Whether to fit the model
`addLegend`	Whether to add a legend to the plot
`...`	Other parameters sent to plot()

This function makes a scatter plot showing the per gene duplication rate versus the total read count.

nothing

# dm is a duplication matrix calculated by analyzeDuprates:
# R> dm <- analyzeDuprates(bamDuprm,gtf,stranded,paired,threads)
attach(dupRadar_examples)

# duprate plot
duprateExpDensPlot(DupMat=dm)