dinucleotideOddsRatio {R453Plus1Toolbox} | R Documentation

## Dinucleotide Odds Ratio

### 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.

[Package R453Plus1Toolbox version 1.38.0 Index]