WfmFit-class {waveTiling} | R Documentation |
class to store model fits in the wavelet-based transcriptome analysis.
## 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)
object |
An instance of |
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)
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betaWav
:Object of class "matrix"
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varbetaWav
:Object of class "matrix"
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smoothPar
:Object of class "matrix"
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varEps
:Object of class "numeric"
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dataOrigSpace
:Object of class "matrix"
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dataWaveletSpace
:Object of class "matrix"
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design.matrix
:Object of class "matrix"
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phenoData
:Object of class "data.frame"
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genome.info
:Object of class "genomeInfo"
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n.levels
:Object of class "numeric"
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probePosition
:Object of class "numeric"
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wave.filt
:Object of class "character"
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Kj
:Object of class "numeric"
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prior
:Object of class "character"
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F
:Object of class "matrix"
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varF
:Object of class "matrix"
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P
:Object of class "numeric"
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Z
:Object of class "matrix"
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noGroups
:Object of class "numeric"
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replics
:Object of class "numeric"
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signature(object = "WfmFit")
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signature(object = "WfmFit")
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signature(object = "WfmFit")
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signature(object = "WfmFit")
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signature(object = "WfmFit")
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signature(object = "WfmFit")
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signature(object = "WfmFit")
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signature(.Object = "WfmFit")
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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.
Kristof De Beuf <kristof.debeuf@ugent.be>
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)