duprateExpPlot: Duplication rate ~ total read count plot

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

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()

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)

ssayols/dupRadar documentation built on Oct. 30, 2024, 4:42 a.m.