seqTools (version 1.6.0)

plotNucFreq: 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

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

See Also

Fastqq-class

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"))
#
plotNucFreq(fq, 2)
# Same plot without x-axis
plotNucFreq(fq, 2, xaxt="n")
#
plotNucFreq(fq, 1, maxx=15)