Class "WfmInf"

Description

class to store outputs from the inference in the wavelet-based transcriptome analysis.

Usage

## Accessors

getAlpha(object)
getDelta(object)
getTwoSided(object)
getSigProbes(object)
getRegions(object)
getGenomicRegions(object)
getFDR(object)
getEff(object)
getVarEff(object)

Arguments

Objects from the Class

Objects can be created by calls of the form new("WfmInf", alpha, delta, two.sided, sigProbes, regions, GlocRegions, FDR, CI, eff, varEff).

Slots

alpha:

Object of class "numeric" ~~

delta:

Object of class "numeric" ~~

two.sided:

Object of class "numeric" ~~

sigProbes:

Object of class "list" ~~

regions:

Object of class "list" ~~

GlocRegions:

Object of class "list" ~~

FDR:

Object of class "matrix" ~~

CI:

Object of class "array" ~~

eff:

Object of class "matrix" ~~

varEff:

Object of class "matrix" ~~

genome.info:

Object of class "genomeInfo" ~~

Methods

getAlpha

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

getDelta

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

getTwoSided

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

getSigProbes

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

getRegions

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

getGenomicRegions

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

getFDR

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

getEff

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

getVarEff

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

getGenomeInfo

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

initialize

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

show

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

plotWfm

signature(fit = "WfmFit", inf = "WfmInf"): ...

getSigGenes

signature(fit = "WfmFit", inf = "WfmInf"): ...

getNonAnnotatedRegions

signature(fit = "WfmFit", inf = "WfmInf"): ...

Accessors

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

getAlpha(x): Extract the alpha level of significance used in the wavelet-based analysis.

getDelta(x): Extract the threshold values used in the wavelet-based transcriptome analysis.

getTwoSided(x): Extract the direction of inference conducted in the wavelet-based transcriptome analysis.

getSigProbes(x): Extract the significant probe ids for the wavelet-based transcriptome analysis.

getRegions(x): Extract the significant regions from the wavelet-based transcriptome analysis. Regions are given in terms of the probe ids they map onto.

getGenomicRegions(x): Extract the significant genomic regions from the wavelet-based transcriptome analysis.

getFDR(x): Extract the FDR for each test in the wavelet-based transcriptome analysis.

getEff(x): Extract the estimated effects or contrasts of the wavelet-based transcriptome analysis.

getVarEff(x): Extract the estimated variances of the effects or contrasts in the wavelet-based transcriptome analysis.

getGenomeInfo(x): Extract the genomic information.

Author(s)

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

Examples

  showClass("WfmInf")
  
  library(waveTilingData)
  data(leafdevInfCompare)
  tt1 <- getAlpha(leafdevInfCompare)
  tt2 <- getDelta(leafdevInfCompare)
  tt3 <- getTwoSided(leafdevInfCompare)
  tt4 <- getSigProbes(leafdevInfCompare)
  tt5 <- getRegions(leafdevInfCompare)
  tt6 <- getGenomicRegions(leafdevInfCompare)
  tt7 <- getFDR(leafdevInfCompare)
  tt8 <- getEff(leafdevInfCompare)
  tt9 <- getVarEff(leafdevInfCompare)
  tt10 <- getGenomeInfo(leafdevInfCompare)