regressResult-class: Class to Contain the Regression Result

Description Creating Objects Slots Methods Author(s) Examples

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

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


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