regressResult-class: Class to Contain the Regression Result

In ArrayTools: geneChip Analysis Package

Description

Class to Contain the Regression Result

Creating Objects

regressResult object is generally created from the regress function See regress

Slots

ID:

contains probe ID/gene ID

foldChange:

contains fold change value

FValue:

contains F statistics

pValue:

contains p value

adjPVal:

contains adjusted p value

contrast:

contains class "contrastMatrix"

regressionMethod:

contains regression method: "limma", "regression", or "permutation"

adjustment:

contains method for multiple comparison adjustment

significantIndex:

contains a logical index indicating sigificant genes

significantPvalueCutoff:

contains a cutoff p-value for choosing significant genes

significantFCCutoff:

contains a fold change cutoff value for choosing significant genes

fileName:

contains a file name for output purpose

annotation:

contains annotation

normalizationMethod:

contains normalization method - for output purpose

filterMethod:

contains filtered method - for output purpose

Methods

adjustment

signature(object = "regressResult")

: access the adjustment slot

getAdjP

signature(object = "regressResult")

: access the adjPVal slot

getAnnotation

signature(object = "regressResult")

: access the annotation slot

getContrast

signature(object = "regressResult")

: access the contrast slot

getF

signature(object = "regressResult")

: access the FValue slot

getFC

signature(object = "regressResult")

: access the foldChange slot

getFCCutoff

signature(object = "regressResult")

: access the significantFCCutoff slot

getFileName

signature(object = "regressResult")

: access the fileName slot

getFilterMethod

signature(object = "regressResult")

: access the filterMethod slot

getID

signature(object = "regressResult")

: access the ID slot

getIndex

signature(object = "regressResult")

: access the significantIndex slot

getNormalizationMethod

signature(object = "regressResult")

: access the normalizationMethod slot

getP

signature(object = "regressResult")

: access the pValue slot

getPCutoff

signature(object = "regressResult")

: access the significantPvalueCutoff slot

Output2HTML

signature(object = "regressResult")

: create HTML file for sigificant genes in regressionResult

regressionMethod

signature(object = "regressResult")

: access the regressionMethod slot

selectSigGene

signature(object = "regressResult")

: select significant genes for regressionResult class

show

signature(object = "regressResult")

: print regressResult

Sort

signature(x = "regressResult")

: sort regressResult

summary

signature(object = "regressResult")

: print the summary for regressResult

Author(s)

Xiwei Wu, Arthur Li

Examples

data(eSetExample)
design<- new("designMatrix", target=pData(eSetExample), covariates = "Treatment")
contrast<- new("contrastMatrix", design.matrix = design, 
    compare1 = "Treated", compare2 = "Control")
result<- regress(eSetExample, contrast)

ArrayTools documentation built on Nov. 8, 2020, 8:13 p.m.