WfmFit-class: Class "WfmFit"

In waveTiling: Wavelet-Based Models for Tiling Array Transcriptome Analysis

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

object

An instance of WfmFit-class.

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 <[e-mail]>

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)

waveTiling documentation built on Oct. 31, 2019, 9:23 a.m.