complexity.dust: Sequence Complexity Using The DUST Algorithm

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

Description

This function evaluates the sequence complexity using the DUST algorithm.

Usage

  complexity.dust(object, xlab="Complexity score (0=high, 100=low)", ylab="Number of sequences", 
    xlim=c(0, 100), col="firebrick1", breaks=100, ...)

Arguments

object	An object of class DNAStringSet, ShortRead or SFFContainer.
xlab	The X axis label.
ylab	The Y axis label.
xlim	The limits of the X axis.
col	The plotting color.
breaks	The number of breaks in the histogram (see ‘hist’).
...	Arguments to be passed to methods, such as graphical parameters (see ‘par’).

Details

The complexity score is based on how often different trinucleotides occur and is scaled between 0 and 100. A sequence of homopolymer repeats (e.g. TTTTTTTTTT) has a score of 100, of dinucleotide repeats (e.g. TATATATATA) has a score around 49, and of trinucleotide repeats (e.g. TAGTAGTAG) has a score around 32. Scores above seven can be considered low-complexity.

Value

A numeric vector containing the complexity score for each sequence.

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.