readPrb: (Legacy) 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, unused.

Value

An object of class QualityScore, or an integer matrix.

Details

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

as="SolexaEncoding"

The ASCII encoding of the maximum per cycle and read quality score is encoded using Solexa conventions.

as="FastqEncoding"

The ASCII encoding of the maximum per cycle and read quality score is encoded using Fastq conventions, i.e., ! has value 0.

as="IntegerEncoding"

The maximum per cycle and read quality score is returned as a in integer value. Values are collated into a matrix with number of rows equal to number of reads, and number of columns equal to number of cycles.

as="array"

The quality scores are not summarized; the return value is an integer array with dimensions corresponding to reads, nucleotides, and cycles.

Examples

Run this code

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

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