Class to Contain the Regression Result Based on An Interaction Model

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Description

Class to Contain the Regression Result Based on An Interaction Model. Interaction is a statistical term refering to a situation when the relationship between the outcome and the variable of the main interest differs at different levels of the extraneous variable

Creating Objects

interactionResult object is generally created from the postInteraction function See postInteraction

Object Components

A list of four or more components. Each component is a reggressResult class. The first component contains all the genes. The second component contains genes with the interaction effect The rest components contains genes with the interaction effect across different levels. Each component contains the result for each level.

Extends

Class "list", from data part. Class "vector", by class "list", distance 2.

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

getLength

signature(object = "interactionResult")

: calculate the length of the interactionResult class

Author(s)

Xiwei Wu, Arthur Li

See Also

regressResult

Examples

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## Creating the interactionREsult takes a few steps:
data(eSetExample)
design.int<- new("designMatrix", target=pData(eSetExample), covariates = c("Treatment", "Group"),
    intIndex = c(1, 2))
contrast.int<- new("contrastMatrix", design.matrix = design.int, interaction=TRUE)
result.int<- regress(eSetExample, contrast.int)
sigResult.int <- selectSigGene(result.int)
intResult <- postInteraction(eSetExample, sigResult.int, mainVar ="Treatment",
   compare1 = "Treated", compare2 = "Control")

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