RocheSet-class

RocheSet

This class is meant to coordinate all data in a Roche (454)
 experiment. See <code>SRSet</code> for additional details.

classes

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

RocheSet-class function

Create objects from this class using one of the <code>RocheSet</code>
 methods documented below

Objects from the Class

<dl> <dt><code>sourcePath</code>:</dt><dd>Object of class <code>"RochePath"</code> The
 file system location of the data used in this experiment.</dd> <dt><code>readIndex</code>:</dt><dd>Object of class <code>"integer"</code> indexing
 reads included in the experiment; see <code>SRSet</code>
 for details on data representation in this class.</dd> <dt><code>readCount</code>:</dt><dd>Object of class <code>"integer"</code>
 containing the number of reads associated with each sample; see
 <code>SRSet</code> for details on data representation in
 this class.</dd> <dt><code>phenoData</code>:</dt><dd>Object of class <code>"AnnotatedDataFrame"</code>
 with as many rows as there are samples, containing information on
 experimental design.</dd> <dt><code>readData</code>:</dt><dd>Object of class <code>"AnnotatedDataFrame"</code>
 containing as many rows as there are reads, containing information
 on each read in the experiment.</dd> </dl>

Slots

Class <code>"SRSet"</code>, directly.
Class <code>".Roche"</code>, directly.
Class <code>".ShortReadBase"</code>, by class "SRSet", distance 2.
Class <code>".ShortReadBase"</code>, by class ".Roche", distance 2.

Extends

No methods defined with class "RocheSet" in the signature; see
 <code>SRSet</code> for inherited methods.

Methods

This class is meant to coordinate all data in a Roche (454)
 experiment. See <code><linkS4class>SRSet</linkS4class></code> for additional details.

RocheSet-class: (Legacy) Roche (454) experiment-wide data container

Description

Arguments

Objects from the Class

Slots

Extends

Methods

See Also

Examples