complexity.dust {R453Plus1Toolbox} | R Documentation

## Sequence Complexity Using The DUST Algorithm

### 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.

[Package R453Plus1Toolbox version 1.30.0 Index]