SRSet-class {ShortRead} | R Documentation

## (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 <mflawrence@fhcrc.org>

### Examples

    showClass("SRSet")

[Package ShortRead version 1.42.0 Index]