geneSignature-class: Class '"geneSignature"'

In sigsquared: Gene signature generation for functionally validated signaling pathways

Description

The geneSignature object contains the necessary elements defining the signaling environment on which a prognostic gene signature will be created.

Objects from the Class

Objects can be created by calls of the form new("geneSignature", ...). Objects all contain 4 slots - geneSet, geneDirect, thresholds, dirMat (unused).

Slots

geneSet:

Object of class "character" ~~

geneDirect:

Object of class "numeric" ~~

thresholds:

Object of class "numeric" ~~

dirMat:

Object of class "matrix" ~~

Methods

analysisPipeline

signature(dataSet = "ExpressionSet", geneSig = "geneSignature"): ...

ensembleAdjustable

signature(dataSet = "ExpressionSet", geneSig = "geneSignature"): ...

ensembleAdjustable

signature(dataSet = "matrix", geneSig = "geneSignature"): ...

getDirect

signature(g = "geneSignature"): ...

getGenes

signature(g = "geneSignature"): ...

getNGenes

signature(g = "geneSignature"): ...

getThresholds

signature(g = "geneSignature"): ...

setDirect

signature(g = "geneSignature", direct = "numeric"): ...

setGenes

signature(g = "geneSignature"): ...

setGeneSignature

signature(g = "geneSignature"): ...

setThresholds

signature(g = "geneSignature"): ...

Author(s)

UnJin lee

References

Lee U, Frankenberger C, Yun J, Bevilacqua E, Caldas C, et al. (2013) A Prognostic Gene Signature for Metastasis-Free Survival of Triple Negative Breast Cancer Patients. PLoS ONE 8(12): e82125. doi:10.1371/journal.pone.0082125

Examples

showClass("geneSignature")

sigsquared documentation built on Nov. 8, 2020, 6:59 p.m.