ShortRead: readQseq – R documentation

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readQseq

(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)

ShortRead

FASTQ input and manipulation

v1.48.0

Artistic-2.0

Authors

Martin Morgan, Michael Lawrence, Simon Anders

Initial release