AlignedRead

An object of class <code>DNAStringSet</code>, containing the
 DNA sequences of the short reads.

sread

An object of class <code>BStringSet</code>, containing the
 identifiers of the short reads. This object is the same length as
 <code>sread</code>.

An object of class <code>BStringSet</code>, containing the
 ASCII-encoded quality scores of the short reads. This object is the
 same length as <code>sread</code>.

quality

A <code>factor</code> describing the particular sequence
 within a set of target sequences (e.g. chromosomes in a genome
 assembly) to which each short read aligns.

chromosome

A <code>integer</code> vector describing the (base pair)
 position at which each short read begins its alignment.

position

A <code>factor</code> describing the strand to which the short
 read aligns.

strand

A <code>numeric</code> vector describing the alignment
 quality.

alignQuality

An <code>AlignedDataFrame</code> with number of rows equal
 to the length of <code>sread</code>, containing additional information
 about alignments.

alignData

This function constructs objects of
 <code>AlignedRead</code>. It will often be more convenient to
 create <code>AlignedRead</code> objects using parsers such as
 <code><a rd-options="" href="/link/readAligned?package=ShortRead&version=1.30.0" data-mini-rdoc="ShortRead::readAligned">readAligned</a></code>.

manip

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

AlignedRead function

This function constructs objects of
 <code><linkS4class>AlignedRead</linkS4class></code>. It will often be more convenient to
 create <code>AlignedRead</code> objects using parsers such as
 <code><a href="readAligned" rd-options="">readAligned</a></code>.

AlignedRead: (Legacy) Construct objects of class "AlignedRead"

Description

Usage

Arguments

Value

See Also