plotPhredQuant: plotPhredQuant: Plots the position wise 10%, 25 %, 50%, 75%...
In seqTools: Analysis of nucleotide, sequence and quality content on fastq files

Description Usage Arguments Value Author(s) See Also Examples

The function creates plots which describes the position wise distribution of phred quantiles in single FASTQ files.

1	plotPhredQuant(object, i, main, ...)

object

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

`i`	`integer`(optional): Index FASTQ file for which phred quantiles are plotted.

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.

None.

Wolfgang Kaisers

Fastqq-class

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"))
#
plotPhredQuant(fq, 2)
# Same plot without x-axis
plotPhredQuant(fq,2, xaxt="n")