SigCheckObject-class: Class '"SigCheckObject"'

In SigCheck: Check a gene signature's prognostic performance against random signatures, known signatures, and permuted data/metadata

Description

The main object containing everything associated with an expression dataset and a gene signatures. Used for subsequent checks of the unique prognostic and/or classification performance of the signature. Based on an ExpressionSet object.

Objects from the Class

The preferred way to create a SigCheckObject is to use the sigCheck function.

Slots

checkType:

Object of class "character" ~~

classes:

Object of class "character" ~~

annotation:

Object of class "character" ~~

survival:

Object of class "character" ~~

signature:

Object of class "vector" ~~

signatureLabels:

Object of class "vector" ~~

validationSamples:

Object of class "vector" ~~

survivalMethod:

Object of class "character" ~~

threshold:

Object of class "ANY" ~~

survivalScores:

Object of class "numeric" ~~

survivalConfusionMatrix:

Object of class "matrix" ~~

survivalClassificationScore:

Object of class "numeric" ~~

survivalPval:

Object of class "numeric", representing performance of the signature in dividing the samples into sets with distinct survival prognosis.

survivalTrainingScores:

Object of class "numeric" ~~

survivalTrainingConfusionMatrix:

Object of class "matrix" ~~

survivalTrainingClassificationScore:

Object of class "numeric" ~~

survivalTrainingPval:

Object of class "numeric" ~~

survivalLabel:

Object of class "character" ~~

timeLabel:

Object of class "character" ~~

classifierMethod:

Object of class "learnerSchema" ~~

sigPerformance:

Object of class "numeric" ~~

confusion:

Object of class "matrix" ~~

modeVal:

Object of class "character" ~~

modePerformance:

Object of class "numeric" ~~

classifier:

Object of class "classifierOutput" ~~

experimentData:

Object of class "MIAME" ~~

assayData:

Object of class "AssayData" ~~

phenoData:

Object of class "AnnotatedDataFrame" ~~

featureData:

Object of class "AnnotatedDataFrame" ~~

protocolData:

Object of class "AnnotatedDataFrame" ~~

.__classVersion__:

Object of class "Versions" ~~

Extends

Class "ExpressionSet", directly. Class "eSet", by class "ExpressionSet", distance 2. Class "VersionedBiobase", by class "ExpressionSet", distance 3. Class "Versioned", by class "ExpressionSet", distance 4.

Methods

No public methods, access slots directly if required.

Note

More methods and documentation coming soon...

Author(s)

Rory Stark

See Also

sigCheck

Examples

showClass("SigCheckObject")

SigCheck documentation built on Nov. 8, 2020, 6:38 p.m.