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

In Bioconductor/ShortRead: FASTQ input and manipulation

(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 <[e-mail]>

Examples

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

Bioconductor/ShortRead documentation built on Nov. 2, 2024, 4:38 p.m.