sigsquared (version 1.4.0)

setGeneSignature: geneSignature functions

Description

The geneSignature object contains the necessary elements defining the signaling environment on which a prognostic gene signature will be created. This collection of functions are used to manipulate or retrieve the data slots of a given geneSignature object.

Usage

setGeneSignature(g, direct=NA, thresholds=c(0), genes=NA, mat=matrix())
setDirect(g, direct)
setThresholds(g, thresholds)
setGenes(g, genes)
getDirect(g)
getThresholds(g)
getGenes(g)
getNGenes(g)

Arguments

g

geneSignature object

direct

vector of -1s or 1s representing down- or up-regulation respectively

thresholds

vector of values containing thresholds for the geneSignature object

genes

character vector of gene names

mat

matrix of interactions between genes (unused)

Value

Examples

## Generate and read out values of a geneSignature object
gs <- setGeneSignature(new("geneSignature"), c(1, 1), c(0, 0), c("BACH1", "RKIP"), matrix())
getDirect(gs)
getThresholds(gs)
getGenes(gs)
getNGenes(gs)