(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

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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

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

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