uniqueFilter

A <code>logical(1)</code> indicating whether uniqueness
 includes the read sequence (<code>withSread=TRUE</code>) or is based only
 on chromosome, position, and strand (<code>withSread=FALSE</code>)

withSread

An optional <code>character(1)</code> object used to over-ride
 the name applied to default filters.

.name

These functions are deprecated, and will become defunct.

ShortRead-deprecated

This package implements sampling, iteration, and input of
FASTQ files. The package includes functions for filtering and
trimming reads, and for generating a quality assessment report.
Data are represented as DNAStringSet-derived objects, and
easily manipulated for a diversity of purposes.  The package
also contains legacy support for early single-end, ungapped
alignment formats.

Bioconductor Package Maintainer

ShortRead

FASTQ input and manipulation

ShortRead-deprecated function

These functions are deprecated, and will become defunct.

ShortRead-deprecated: Deprecated functions from the ShortRead package

Description

Usage

Arguments

Details