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, batchSize=NA, ...)

### Arguments

`x` | A `DNAStringSet` object, or object derived from `ShortRead`, containing a collection of reads to be summarized.
`batchSize` | `NA` or an `integer(1)` vector indicating the maximum number of reads to be processed at any one time.
`...` | 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).

The `batchSize` argument can be used to reduce the memory requirements of the algorithm by processing the `x` argument in batches of the specified size. Smaller batch sizes use less memory, but are computationally less efficient.

### 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 1.45.4 Index]