Duplication rate ~ total read count plot

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Description

duprateExpDensPlot Duplication rate ~ total read count plot

Usage

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

Arguments

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()

Details

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

Value

nothing

Examples

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

# duprate plot
duprateExpDensPlot(DupMat=dm)

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