readBaseQuality {ShortRead} | R Documentation

## (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>

### See Also

A `ShortReadQ` object.

`readXStringColumns`, `readPrb`

### Examples

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

[Package ShortRead version 1.38.0 Index]