(Legacy) Read short reads and their quality scores into R representations

Description

readBaseQuality reads all base call files in a directory dirPath whose file name matches seqPattern and all quality score files whose name matches prbPattern, returning a compact internal representation of the sequences, and quality scores in the files. Methods read all files into a single R object.

Usage

1
2
3
4
readBaseQuality(dirPath, ...)
## S4 method for signature 'character'
readBaseQuality(dirPath, seqPattern=character(0),
prbPattern=character(0), type=c("Solexa"), ...)

Arguments

dirPath

A character vector (or other object; see methods defined on this generic) giving the directory path (relative or absolute) of files to be input.

seqPattern

The (grep-style) pattern describing base call file names to be read. The default (character(0)) results in (attempted) input of all files in the directory.

prbPattern

The (grep-style) pattern describing quality score file names to be read. The default (character(0)) results in (attempted) input of all files in the directory.

type

The type of file to be parsed. Supported types include: Solexa: parse reads and their qualities from _seq.txt and _prb.txt-formatted files, respectively.

...

Additional arguments, perhaps used by methods.

Value

A single R object (e.g., ShortReadQ) containing sequences and qualities of all files in dirPath matching seqPattern and prbPattern respectively. There is no guarantee of order in which files are read.

Author(s)

Patrick Aboyoun <paboyoun@fhcrc.org>

See Also

A ShortReadQ object.

readXStringColumns, readPrb

Examples

1
2
sp <- SolexaPath(system.file("extdata", package="ShortRead"))
readBaseQuality(sp, seqPattern="s_1.*_seq.txt", prbPattern="s_1.*_prb.txt")

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.