accessors: (Legacy) Accessors for ShortRead classes

In ShortRead: FASTQ input and manipulation

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 documentation built on Nov. 8, 2020, 8:02 p.m.