ShortRead: accessors – R documentation

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accessors

(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, ...)
## 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))

ShortRead

FASTQ input and manipulation

v1.48.0

Artistic-2.0

Authors

Martin Morgan, Michael Lawrence, Simon Anders

Initial release