readQseq {ShortRead} | R Documentation

## (Legacy) Read Solexa qseq files as fastq-style quality scores

### Description

`readQseq` reads all files matching `pattern` in a directory into a single `ShortReadQ`-class object. Information on machine, lane, tile, x, and y coordinates, filtering status, and read number are not returned (although filtering status can be used to selectively include reads as described below).

### Usage

    readQseq(dirPath, pattern = character(0), ...,
             as=c("ShortReadQ", "DataFrame", "XDataFrame"),
             filtered=FALSE,
             verbose=FALSE)

### Arguments

`dirPath` | Directory path or other object (e.g., `SolexaPath`) for which methods are defined.
`pattern` | Regular expression matching names of `_qseq` files to be summarized.
`...` | Additional argument, passed to I/O functions.
`as` | `character(1)` indicating the class of the return type. “XDataFrame” is included for backward compatibility, but is no longer supported.
`filtered` | `logical(1)` indicating whether to include only those reads passing Solexa filtering?
`verbose` | `logical(1)` indicating whether to report on progress during evaluation.

### Value

An object of class `ShortReadQ`.

### Author(s)

Martin Morgan <mtmorgan@fhcrc.org>

### Examples

    fl <- system.file("extdata", package="ShortRead")
    sp <- SolexaPath(fl)
    readQseq(sp)

[Package ShortRead version 1.45.4 Index]