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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(waveTiling)
Loading required package: oligo
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: oligoClasses
Welcome to oligoClasses version 1.34.0
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector
================================================================================
Welcome to oligo version 1.36.1
================================================================================
Loading required package: GenomeGraphs
Loading required package: biomaRt
Loading required package: grid
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/waveTiling/WaveTilingFeatureSet-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: WaveTilingFeatureSet-class
> ### Title: Class "WaveTilingFeatureSet"
> ### Aliases: WaveTilingFeatureSet-class WaveTilingFeatureSet
> ###   initialize,WaveTilingFeatureSet-method
> ###   show,WaveTilingFeatureSet-method addPheno,WaveTilingFeatureSet-method
> ###   bgCorrQn,WaveTilingFeatureSet-method
> ###   filterOverlap,WaveTilingFeatureSet-method getGroupNames
> ###   getGroupNames,WaveTilingFeatureSet-method getNoGroups
> ###   getNoGroups,WaveTilingFeatureSet-method getReplics
> ###   getReplics,WaveTilingFeatureSet-method
> ###   selectProbesFromTilingFeatureSet,WaveTilingFeatureSet-method
> ###   wfm.fit,WaveTilingFeatureSet-method
> ### Keywords: classes
> 
> ### ** Examples
> 
>   showClass("WaveTilingFeatureSet")
Class "WaveTilingFeatureSet" [package "waveTiling"]

Slots:
                                                               
Name:        manufacturer      intensityFile          assayData
Class:          character          character          AssayData
                                                               
Name:           phenoData        featureData     experimentData
Class: AnnotatedDataFrame AnnotatedDataFrame              MIAxE
                                                               
Name:          annotation       protocolData  .__classVersion__
Class:          character AnnotatedDataFrame           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
>   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)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>