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Last data update: 2014.03.03

R: plotGCcontent: Plots the proportions of relative GC content...

plotGCcontent

R Documentation

plotGCcontent: Plots the proportions of relative GC content for all FASTQ files.

Description

The function creates plots on proportions of relative GC content. For each FASTQ file from wich data is contained, one separate line is plotted. A value of 0.1 at the proportion of 40 says that 0.1 % of the reads have 40 % GC content.

Usage

plotGCcontent(object, main, ...)

Arguments

object

Fastqq: Object which contains collected values from nFiles FASTQ files.

main

integer(optional): The main title displayed on top of the plot. When missing, a standard text is printed.

...

Other arguments which are passed to the internally called plot function.

Details

The area under each plotted line adds up to 1.

Value

None.

Author(s)

Wolfgang Kaisers

Examples

basedir <- system.file("extdata", package="seqTools")
setwd(basedir)
fq <- fastqq(c("g4_l101_n100.fq.gz", "g5_l101_n100.fq.gz"), k=4, 
    probeLabel=c("g4", "g5"))
#
plotGCcontent(fq)

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.
You are welcome to redistribute it under certain conditions.
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(seqTools)
Loading required package: zlibbioc
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/seqTools/plotGCcontent.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotGCcontent
> ### Title: plotGCcontent: Plots the proportions of relative GC content for
> ###   all FASTQ files.
> ### Aliases: plotGCcontent plotGCcontent-methods
> ###   plotGCcontent,Fastqq-method
> ### Keywords: plotGCcontent kmer
> 
> ### ** Examples
> 
> basedir <- system.file("extdata", package="seqTools")
> setwd(basedir)
> fq <- fastqq(c("g4_l101_n100.fq.gz", "g5_l101_n100.fq.gz"), k=4, 
+     probeLabel=c("g4", "g5"))
[fastqq] File ( 1/2) 'g4_l101_n100.fq.gz'	done.
[fastqq] File ( 2/2) 'g5_l101_n100.fq.gz'	done.
> #
> plotGCcontent(fq)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>