Class "WaveTilingFeatureSet"

Description

Class to store expression and phenotypic data from a tiling array experiment, used as input for the wavelet-based transcriptome analysis.

Usage

## Accessors

getGroupNames(object)
getNoGroups(object)
getReplics(object)

Arguments

Objects from the Class

Objects can be created by calls of the form new("WaveTilingFeatureSet").

Slots

manufacturer:

Object of class "character" ~~

intensityFile:

Object of class "character" ~~

assayData:

Object of class "AssayData" ~~

phenoData:

Object of class "AnnotatedDataFrame" ~~

featureData:

Object of class "AnnotatedDataFrame" ~~

experimentData:

Object of class "MIAME" ~~

annotation:

Object of class "character" ~~

protocolData:

Object of class "AnnotatedDataFrame" ~~

.__classVersion__:

Object of class "Versions" ~~

Extends

Class "TilingFeatureSet", directly. Class "FeatureSet", by class "TilingFeatureSet", distance 2. Class "NChannelSet", by class "TilingFeatureSet", distance 3. Class "eSet", by class "TilingFeatureSet", distance 4. Class "VersionedBiobase", by class "TilingFeatureSet", distance 5. Class "Versioned", by class "TilingFeatureSet", distance 6.

Methods

addPheno

signature(object = "WaveTilingFeatureSet"): ...

bgCorrQn

signature(object = "WaveTilingFeatureSet"): ...

filterOverlap

signature(object = "WaveTilingFeatureSet"): ...

getGroupNames

signature(object = "WaveTilingFeatureSet"): ...

getNoGroups

signature(object = "WaveTilingFeatureSet"): ...

getReplics

signature(object = "WaveTilingFeatureSet"): ...

selectProbesFromTilingFeatureSet

signature(object = "WaveTilingFeatureSet"): ...

wfm.fit

signature(object = "WaveTilingFeatureSet"): ...

Accessors

In the following code snippets, x is a WaveTilingFeatureSet object. The described accessors are specific for WaveTilingFeatureSet-class objects. Other inherited accessors work as expected on this class.

getGroupNames(x): Extract the group or sample names in the tiling array experiment.

getNoGroups(x): Extract the number of groups or samples in the tiling array experiment.

getReplics(x): Extract the number of replicates in the tiling array experiment.

Author(s)

Kristof De Beuf <kristof.debeuf@ugent.be>

Examples

  showClass("WaveTilingFeatureSet")
  library(waveTilingData)
  data(leafdev)
  leafdev <- as(leafdev,"WaveTilingFeatureSet")
  leafdev <- addPheno(leafdev,noGroups=6,groupNames=c("day8","day9","day10","day11","day12","day13"),replics=rep(3,6))
  tt1 <- getGroupNames(leafdev)
  tt2 <- getNoGroups(leafdev)
  tt3 <- getReplics(leafdev)