dinucleotideOddsRatio: Dinucleotide Odds Ratio

Description Usage Arguments Details Value Author(s) References

View source: R/qualityControl.R

Description

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

Usage

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  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. 1, 2018, 2:27 a.m.