regressResult-class {ArrayTools}R Documentation

Class to Contain the Regression Result

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)

[Package ArrayTools version 1.2.1 Index]