dinucleotideOddsRatio {R453Plus1Toolbox} | R Documentation |
This function calculates the dinucleotide odds ratio for each of the sixtheen possible dinucleotides.
dinucleotideOddsRatio(object, xlab="Under-/over-representation of dinucleotides", col="firebrick1", ...)
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’). |
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.
A matrix with sixtheen columns, one for each dinucleotide, containing the dinucleotide odds ratio values for each sequence in a seperate row.
Christian Ruckert
Schmieder R. (2011) Quality control and preprocessing of metagenomic datasets. Bioinformatics, 2011 Mar 15;27(6):863-4.