R: plotNucFreq: Plots the position wise relative nucleotide...
plotNucFreq
R Documentation
plotNucFreq: Plots the position wise relative nucleotide content for
nucleotides 'A','C','G','T'.
Description
The function creates plots on position wise relative
nucleotide content single FASTQ files.
Usage
plotNucFreq(object, i, main, maxx, ...)
Arguments
object
Fastqq: Object which contains collected values from
nFiles FASTQ files.
i
integer(optional): Index FASTQ file for which nucleotide
frequencies are plotted.
main
integer(optional): The main title displayed on top of
the plot. When missing, a standard text is printed.
maxx
integer(optional): Determines the maximum sequence
position for which counts are plotted. Small values (e.g. 15) allow
plotting the distribution on the first nucleotides at larger resolution
(see reference).
...
Other arguments which are passed to the internally called plot
function.
Value
None.
Author(s)
Wolfgang Kaisers
References
Hansen KD, Brenner SE, Dudoit S.
Biases in Illumina transcriptome sequencing caused by random hexamer priming.
Nucleic Acids Research 2010 Vol.38 No.12 e131, doi: 10.1093/nar/gkq224
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/plotNucFreq.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotNucFreq
> ### Title: plotNucFreq: Plots the position wise relative nucleotide content
> ### for nucleotides 'A','C','G','T'.
> ### Aliases: plotNucFreq plotNucFreq-methods plotNucFreq,Fastqq-method
> ### Keywords: plotNucFreq 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.
> #
> plotNucFreq(fq, 2)
> # Same plot without x-axis
> plotNucFreq(fq, 2, xaxt="n")
> #
> plotNucFreq(fq, 1, maxx=15)
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.
