Class "WfmFit"

Description

class to store model fits in the wavelet-based transcriptome analysis.

Usage

## Accessors

getProbePosition(object)
getNoProbes(object)
getBetaWav(object)
getVarBetaWav(object)
getSmoothPar(object)
getVarEps(object)
getGenomeInfo(object)
getMinPos(object)
getMaxPos(object)
getNoLevels(object)
getDesignMatrix(object)
getPhenoInfo(object)
getDataOrigSpace(object)
getDataWaveletSpace(object)
getWaveletFilter(object)
getKj(object)
getPrior(object)
getF(object)
getVarF(object)

Arguments

Objects from the Class

Objects can be created by calls of the form new("WfmFit", betaWav, varbetaWav, smoothPar, varEps, dataOrigSpace, dataWaveletSpace, design.matrix, phenoData, genome.info, n.levels, probePosition, wave.filt, Kj, prior, F, varF, P, Z, noGroups, replics).

Slots

betaWav:

Object of class "matrix" ~~

varbetaWav:

Object of class "matrix" ~~

smoothPar:

Object of class "matrix" ~~

varEps:

Object of class "numeric" ~~

dataOrigSpace:

Object of class "matrix" ~~

dataWaveletSpace:

Object of class "matrix" ~~

design.matrix:

Object of class "matrix" ~~

phenoData:

Object of class "data.frame" ~~

genome.info:

Object of class "genomeInfo" ~~

n.levels:

Object of class "numeric" ~~

probePosition:

Object of class "numeric" ~~

wave.filt:

Object of class "character" ~~

Kj:

Object of class "numeric" ~~

prior:

Object of class "character" ~~

F:

Object of class "matrix" ~~

varF:

Object of class "matrix" ~~

P:

Object of class "numeric" ~~

Z:

Object of class "matrix" ~~

noGroups:

Object of class "numeric" ~~

replics:

Object of class "numeric" ~~

Methods

getBetaWav

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

getChromosome

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

getDataOrigSpace

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

getDataWaveletSpace

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

getDesignMatrix

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

getF

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

getGenomeInfo

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

getKj

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

getMaxPos

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

getMinPos

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

getNoLevels

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

getNoProbes

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

getPhenoInfo

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

getPrior

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

getProbePosition

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

getSmoothPar

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

getStrand

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

getVarBetaWav

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

getVarEps

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

getVarF

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

getWaveletFilter

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

initialize

signature(.Object = "WfmFit"): ...

show

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

wfm.inference

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

Accessors

In the following code snippets, x is a WfmFit object.

getBetaWav(x): Extract the fitted effect functions in the wavelet space.

getChromsome(x): Extract the chromosome identifiers.

getDataOrigSpace(x): Extract the raw expression data in the original data space.

getDataWaveletSpace(x): Extract the raw data in the wavelet space, i.e. the wavelet coefficients.

getDesignMatrix(x): Extract the design matrix used in the wavelet-based analysis.

getF(x): Extract the fitted functional effects in the original data space.

getGenomeInfo(x): Extract the genomic information.

getKj(x): Extract the number of wavelet coefficients estimated per wavelet level.

getMaxPos(x): Extract the maximum genomic probe position.

getMinPos(x): Extract the minimum genomic probe position.

getNoLevels(x): Extract the number of levels in in the wavelet decomposition when fitting the wavelet-based functional model.

getNoProbes(x): Extract the number of probes.

getPhenoInfo(x): Extract the phenotypic information for the tiling array experiment.

getPrior(x): Extract the the type or distribution of the prior imposed on the functional effects in the wavelet space.

getProbePosition(x): Extract probe position.

getSmoothPar(x): Extract the estimated smoothing parameters that control the regularization of the effect functions in the wavelet space.

getStrand(x): Extract the strand orientation info.

getVarBetaWav(x): Extract the variance of the fitted effect functions in the wavelet space.

getVarEps(x): Extract the estimated residual variance in the wavelet space. One variance parameter is estimated per wavelet level.

getVarF(x): Extract the variance of the fitted functional effects in the original data space.

getWaveletFilter(x): Extract the wavelet filter used to transform the data from the original space to the wavelet space.

Author(s)

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

Examples

  showClass("WfmFit")
  
  library(waveTilingData)
  data(leafdevFit)
  tt1 <- getBetaWav(leafdevFit)
  tt2 <- getChromosome(leafdevFit)
  tt3 <- getDataOrigSpace(leafdevFit)
  tt4 <- getDataWaveletSpace(leafdevFit)
  tt5 <- getDesignMatrix(leafdevFit)
  tt6 <- getF(leafdevFit)
  tt7 <- getGenomeInfo(leafdevFit)
  tt8 <- getKj(leafdevFit)
  tt9 <- getMaxPos(leafdevFit)
  tt10 <- getMinPos(leafdevFit)
  tt11 <- getNoLevels(leafdevFit)
  tt12 <- getNoProbes(leafdevFit)
  tt13 <- getPhenoInfo(leafdevFit)
  tt14 <- getPrior(leafdevFit)
  tt15 <- getProbePosition(leafdevFit)
  tt16 <- getSmoothPar(leafdevFit)
  tt17 <- getStrand(leafdevFit)
  tt18 <- getVarBetaWav(leafdevFit)
  tt19 <- getVarEps(leafdevFit)
  tt20 <- getVarF(leafdevFit)
  tt21 <- getWaveletFilter(leafdevFit)

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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
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/WfmFit-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: WfmFit-class
> ### Title: Class "WfmFit"
> ### Aliases: WfmFit-class WfmFit show,WfmFit-method
> ###   initialize,WfmFit-method getProbePosition
> ###   getProbePosition,WfmFit-method getNoProbes getNoProbes,WfmFit-method
> ###   getBetaWav getBetaWav,WfmFit-method getVarBetaWav
> ###   getVarBetaWav,WfmFit-method getSmoothPar getSmoothPar,WfmFit-method
> ###   getVarEps getVarEps,WfmFit-method getGenomeInfo
> ###   getGenomeInfo,WfmFit-method getChromosome,WfmFit-method
> ###   getStrand,WfmFit-method getMinPos getMinPos,WfmFit-method getMaxPos
> ###   getMaxPos,WfmFit-method getNoLevels getNoLevels,WfmFit-method
> ###   getDesignMatrix getDesignMatrix,WfmFit-method getPhenoInfo
> ###   getPhenoInfo,WfmFit-method getDataOrigSpace
> ###   getDataOrigSpace,WfmFit-method getDataWaveletSpace
> ###   getDataWaveletSpace,WfmFit-method getWaveletFilter
> ###   getWaveletFilter,WfmFit-method getKj getKj,WfmFit-method getPrior
> ###   getPrior,WfmFit-method getF getF,WfmFit-method getVarF
> ###   getVarF,WfmFit-method wfm.inference,WfmFit-method
> ### Keywords: classes
> 
> ### ** Examples
> 
>   showClass("WfmFit")
Class "WfmFit" [package "waveTiling"]

Slots:
                                                                          
Name:           betaWav       varbetaWav        smoothPar           varEps
Class:           matrix           matrix           matrix          numeric
                                                                          
Name:     dataOrigSpace dataWaveletSpace    design.matrix        phenoData
Class:           matrix           matrix           matrix       data.frame
                                                                          
Name:       genome.info         n.levels    probePosition        wave.filt
Class:       GenomeInfo          numeric           vector        character
                                                                          
Name:                Kj            prior                F             varF
Class:          numeric        character           matrix           matrix
                                                                          
Name:                 P                Z         noGroups          replics
Class:          numeric           matrix          numeric          numeric

Known Subclasses: "WfmFitFactor", "WfmFitTime", "WfmFitCircadian", "WfmFitCustom"
>   
>   library(waveTilingData)
>   data(leafdevFit)
>   tt1 <- getBetaWav(leafdevFit)
>   tt2 <- getChromosome(leafdevFit)
>   tt3 <- getDataOrigSpace(leafdevFit)
>   tt4 <- getDataWaveletSpace(leafdevFit)
>   tt5 <- getDesignMatrix(leafdevFit)
>   tt6 <- getF(leafdevFit)
>   tt7 <- getGenomeInfo(leafdevFit)
>   tt8 <- getKj(leafdevFit)
>   tt9 <- getMaxPos(leafdevFit)
>   tt10 <- getMinPos(leafdevFit)
>   tt11 <- getNoLevels(leafdevFit)
>   tt12 <- getNoProbes(leafdevFit)
>   tt13 <- getPhenoInfo(leafdevFit)
>   tt14 <- getPrior(leafdevFit)
>   tt15 <- getProbePosition(leafdevFit)
>   tt16 <- getSmoothPar(leafdevFit)
>   tt17 <- getStrand(leafdevFit)
>   tt18 <- getVarBetaWav(leafdevFit)
>   tt19 <- getVarEps(leafdevFit)
>   tt20 <- getVarF(leafdevFit)
>   tt21 <- getWaveletFilter(leafdevFit)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>