plotPhredQuant: plotPhredQuant: Plots the position wise 10%, 25 %, 50%, 75%...

In wokai/seqTools: Analysis of nucleotide, sequence and quality content on fastq files.

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")

wokai/seqTools documentation built on May 4, 2019, 9:46 a.m.