readPrb {ShortRead} | R Documentation

## (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.

### 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.

### 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 1.48.0 Index]