plotPhredQuant {seqTools}R Documentation

plotPhredQuant: Plots the position wise 10%, 25 %, 50%, 75% and 90 % quantiles of phred values.

Description

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

Usage

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

Arguments

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.

Value

None.

Author(s)

Wolfgang Kaisers

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"))
#
plotPhredQuant(fq, 2)
# Same plot without x-axis
plotPhredQuant(fq,2, xaxt="n")
[Package seqTools version 1.16.0 Index]