ShortRead: readBaseQuality – R documentation

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readBaseQuality

(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

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>

Examples

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

ShortRead

FASTQ input and manipulation

v1.48.0

Artistic-2.0

Authors

Martin Morgan, Michael Lawrence, Simon Anders

Initial release