setGeneSignature {sigsquared} | R Documentation |
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.
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)
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) |
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
UnJin Lee
## 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)