accessors {ShortRead} | R Documentation

## (Legacy) Accessors for ShortRead classes

### Description

These functions and generics define ‘accessors’ (to get and set values) for objects in the ShortRead package; methods defined in other packages may have additional meaning.

### Usage

    ## SRVector
    vclass(object, ...)
    ## ShortRead / ShortReadQ
    sread(object, ...)
    id(object, ...)
    ## AlignedRead
    chromosome(object, ...)
    position(object, ...)
    alignQuality(object, ...)
    alignData(object, ...)
    ## Solexa
    experimentPath(object, ...)
    dataPath(object, ...)
    scanPath(object, ...)
    imageAnalysisPath(object, ...)
    baseCallPath(object, ...)
    analysisPath(object, ...)
    ## SolexaSet
    solexaPath(object, ...)
    laneDescription(object, ...)
    laneNames(object, ...)

### Arguments

`object` | An object derived from class `ShortRead`. See help pages for individual objects, e.g., `ShortReadQ`. The default is to extract the contents of a slot of the corresponding name (e.g., slot `sread`) from `object`.
`...` | Additional arguments passed to the accessor. The default definitions do not make use of additional arguments.

### Value

Usually, the value of the corresponding slot, or other simple content described on the help page of `object`.

### Author(s)

Martin Morgan

### Examples

    sp <- SolexaPath(system.file('extdata', package='ShortRead'))
    experimentPath(sp)
    basename(analysisPath(sp))

[Package ShortRead version 1.36.1 Index]