duprateExpPlot: Duplication rate ~ total read count plot

Description

duprateExpPlot Duplication rate ~ total read count plot

Usage

duprateExpPlot(DupMat, tNoAlternative = TRUE, tRPKM = TRUE,
  tRPKMval = 0.5, addLegend = TRUE, ...)

Arguments

DupMat

The duplication matrix calculated by analyzeDuprates

tNoAlternative

Display threshold of 1000 reads per kilobase

tRPKM

Display threshold at a given RPKM level

tRPKMval

The given RPKM level

addLegend

Whether to add a legend to the plot

...

Other parameters sent to smoothScatter()

Value

nothing

Details

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

Examples

Run this code

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

# duprate plot
duprateExpPlot(DupMat=dm)