readPrb {ShortRead}R Documentation

Read Solexa prb files as fastq-style quality scores

Description

readPrb reads all _prb.txt files in a directory into a single object. Most methods (see details) do this by identifying the maximum base call quality for each cycle and read, and representing this as an ASCII-encoded character string.

Usage

readPrb(dirPath, pattern = character(0), ...)

Arguments

dirPath Directory path or other object (e.g., SolexaPath for which methods are defined.
pattern Regular expression matching names of _prb files to be summarized.
... Additional arguments, e.g., to srapply, used during evaluation.

Details

The readPrb,character-method contains an arugment as that determines the value of the returned object, as follows.

Value

An object of class QualityScore, or an integer matrix.

Author(s)

Martin Morgan <mtmorgan@fhcrc.org>

Examples

fl <- system.file("extdata", package="ShortRead")
sp <- SolexaPath(fl)
readPrb(sp, "s_1.*_prb.txt") # all tiles to a single file

[Package ShortRead version 1.2.1 Index]