R: Duplication rate ~ total reads per kilobase (RPK) boxplot
duprateExpBoxplot
R Documentation
Duplication rate ~ total reads per kilobase (RPK) boxplot
Description
duprateExpBoxplot Duplication rate ~ total reads per kilobase (RPK) boxplot
Usage
duprateExpBoxplot(DupMat, stepSize = 0.05, ...)
Arguments
DupMat
The duplication matrix calculated by analyzeDuprates
stepSize
Expression bin seze for the boxplot
...
Other params sent to boxplot
Details
This function makes a boxplot showing the distribution of per gene duplication rate versus
the reads per kilobase (RPK) inside gene expression bins.
Value
nothing
Examples
# dm is a duplication matrix calculated by analyzeDuprates:
# R> dm <- analyzeDuprates(bamDuprm,gtf,stranded,paired,threads)
attach(dupRadar_examples)
# duprate boxplot
duprateExpBoxplot(DupMat=dm)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(dupRadar)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/dupRadar/duprateExpBoxplot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: duprateExpBoxplot
> ### Title: Duplication rate ~ total reads per kilobase (RPK) boxplot
> ### Aliases: duprateExpBoxplot
>
> ### ** Examples
>
> # dm is a duplication matrix calculated by analyzeDuprates:
> # R> dm <- analyzeDuprates(bamDuprm,gtf,stranded,paired,threads)
> attach(dupRadar_examples)
>
> # duprate boxplot
> duprateExpBoxplot(DupMat=dm)
>
>
>
>
>
> dev.off()
null device
1
>