duprateExpDensPlot: Duplication rate ~ total read count plot

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

Duplication rate ~ total read count plot

Description

duprateExpDensPlot Duplication rate ~ total read count plot

Usage

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

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

# duprate plot
duprateExpDensPlot(DupMat=dm)

imbforge/dupRadar documentation built on Oct. 18, 2023, 8:54 a.m.