nucleotideCharts: Nucleotide Charts

In R453Plus1Toolbox: A package for importing and analyzing data from Roche's Genome Sequencer System

Description

This function plots the relative frequency of the four bases for each position in the sequences.

Usage

  nucleotideCharts(object, range=0.95, linetypes=c(A="l", C="l", G="l", T="l", N="l"), 
    linecols=c(A="black", C="red", G="blue", T="green", N="grey70"), xlab="Position", 
    ylab="Frequency", ...)

Arguments

object	An object of class DNAStringSet, ShortRead or SFFContainer.
range	An integer vector of length one or two. If length one only bases up to the percent quantile of read lengths defined by the given value are shown. A vector of length two gives the start and end base between which the nucleotide frequencies are plotted.
linetypes	The line types used for the four nucleotids + N, see (see ‘par’)
linecols	The colors in which the four nucleotids + N should be plotted.
xlab	The X axis label.
ylab	The Y axis label.
...	Arguments to be passed to methods, such as graphical parameters (see ‘par’).

Author(s)

Christian Ruckert

R453Plus1Toolbox documentation built on Nov. 8, 2020, 5:59 p.m.