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Last data update: 2014.03.03

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

plotPhredQuant

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

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")

Results


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/plotPhredQuant.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotPhredQuant
> ### Title: plotPhredQuant: Plots the position wise 10%, 25 %, 50%, 75% and
> ###   90 % quantiles of phred values.
> ### Aliases: plotPhredQuant plotPhredQuant-methods
> ###   plotPhredQuant,Fastqq-method
> ### Keywords: plotPhredQuant 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.
> #
> plotPhredQuant(fq, 2)
> # Same plot without x-axis
> plotPhredQuant(fq,2, xaxt="n")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>