dustyScore {ShortRead}R Documentation

Summarize low-complexity sequences

Description

dustyScore identifies low-complexity sequences, in a manner inspired by the dust implementation in BLAST.

Usage


dustyScore(x, ...)

Arguments

x A DNAStringSet object, or object derived from ShortRead, containing a collection of reads to be summarized.
... Additional arguments, not currently used.

Details

The following methods are defined:

dustyScore
signature(x = "DNAStringSet"): operating on an object derived from class DNAStringSet.
dustyScore
signature(x = "ShortRead"): operating on the sread of an object derived from class ShortRead.

The dust-like calculations used here are as implemented at https://stat.ethz.ch/pipermail/bioc-sig-sequencing/2009-February/000170.html. Scores range from 0 (all triplets unique) to the square of the width of the longest sequence (poly-A, -C, -G, or -T).

Value

A vector of numeric scores, with length equal to the length of x.

Author(s)

Herve Pages (code); Martin Morgan

References

Morgulis, Getz, Schaffer and Agarwala, 2006. WindowMasker: window-based masker for sequenced genomes, Bioinformatics 22: 134-141.

See Also

The WindowMasker supplement defining dust ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/windowmasker/windowmasker_suppl.pdf

Examples

sp <- SolexaPath(system.file('extdata', package='ShortRead'))
rfq <- readFastq(analysisPath(sp), pattern="s_1_sequence.txt")
range(dustyScore(rfq))

[Package ShortRead version 1.2.1 Index]