WfmInf-class: Class "WfmInf"

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

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

object

An instance of WfmInf-class.

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 <[e-mail]>

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)

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