setGeneSignature: geneSignature functions

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. 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

All setting functions return objects of class geneSignature. getDirect yields a vector of -1s or 1s, getThesholds yields a vector of theshold values, getGenes yields a character vector of gene names, getNGenes yields the number of genes in the geneSignature

Author(s)

UnJin Lee

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)

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