Description Usage Arguments Objects from the Class Slots Methods Accessors Author(s) Examples
class to store model fits in the wavelet-based transcriptome analysis.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | ## 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)
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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)
.
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"
~~
Z
:Object of class "matrix"
~~
noGroups
:Object of class "numeric"
~~
replics
:Object of class "numeric"
~~
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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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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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>
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 | 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)
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