SRSet-class: (Legacy) A base class for Roche experiment-wide data

In Bioconductor/ShortRead: FASTQ input and manipulation

(Legacy) A base class for Roche experiment-wide data

Description

This class coordinates phenotype (sample) and sequence data, primarily as used on the Roche platform.

Conceptually, this class has reads from a single experiment represented as a long vector, ordered by sample. The readCount slot indicates the number of reads in each sample, so that the sum of readCount is the total number of reads in the experiment. The readIndex field is a light-weight indicator of which reads from all those available that are currently referenced by the SRSet.

Objects from the Class

Objects of this class are not usually created directly, but instead are created by a derived class, e.g., RocheSet.

Slots

sourcePath:

Object of class "ExperimentPath", containing the directory path where sequence files can be found.

readIndex:

Object of class "integer" indicating specific sequences included in the experiment.

readCount:

Object of class "integer" containing the number of reads in each sample included in the experiment. The sum of this vector is the total number of reads.

phenoData:

Object of class "AnnotatedDataFrame" describing each sample in the experiment. The number of rows of phenoData equals the number of elements in readCount.

readData:

Object of class "AnnotatedDataFrame" containing annotations on all reads.

Extends

Class ".ShortReadBase", directly.

Methods

experimentPath

signature(object = "SRSet"): return the ExperimentPath associated with this object.

phenoData

signature(object = "SRSet"): return the phenoData associated with this object.

readCount

signature(object="SRSet"):

readIndex

signature(object="SRSet"):

readData

signature(object="SRSet"):

sourcePath

signature(object="SRSet"): Retrieve the corresponding slot from object.

show

signature(object = "SRSet"): display the contents of this object.

detail

signature(x = "SRSet"): provide more extensive information on the object.

Author(s)

Michael Lawrence <[e-mail]>

Examples

showClass("SRSet")

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