duprateExpPlot: Duplication rate ~ total read count plot

In dupRadar: Assessment of duplication rates in RNA-Seq datasets

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()

Details

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

Value

nothing

Examples

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

# duprate plot
duprateExpPlot(DupMat=dm)

Example output

dupRadar documentation built on Nov. 8, 2020, 5:41 p.m.