dinucleotideOddsRatio: Dinucleotide Odds Ratio

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

Description

This function calculates the dinucleotide odds ratio for each of the sixtheen possible dinucleotides.

Usage

  dinucleotideOddsRatio(object, xlab="Under-/over-representation of dinucleotides", 
    col="firebrick1", ...)

Arguments

object	An object of class DNAStringSet, ShortRead or SFFContainer.
xlab	The X axis label.
col	The plotting color.
...	Arguments to be passed to methods, such as graphical parameters (see ‘par’).

Details

The dinucleotide odds ratio assigns a value between 0 and 2 to each of the sixtheen possible dinucleotides (AA, AC, AG, AT, CA, CC, CG, CT, GA, GC, GG, GT, TA, TC, TG, TT). For values below 1 the dinucleotide is under-represented compared to the randomly expected frequency of this dinucleotide in a sequence of the given length and with the given frequencies of the four nucleotides (A, C, G, T). For values above 1 this dinucleotide is over-represented.

Value

A matrix with sixtheen columns, one for each dinucleotide, containing the dinucleotide odds ratio values for each sequence in a seperate row.

Author(s)

Christian Ruckert

References

Schmieder R. (2011) Quality control and preprocessing of metagenomic datasets. Bioinformatics, 2011 Mar 15;27(6):863-4.

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