incidence-methods: Methods for Constructing Incidence Matricies Between GeneSets

In Bioconductor/GSEABase: Gene set enrichment data structures and methods

Methods for Constructing Incidence Matricies Between GeneSets

Description

An incidence matrix summarizes shared membership of gene identifiers across (pairs of) gene sets.

Methods

The return value is a matrix with rows representing gene sets and columns genes.

signature(x="GeneSet", ...) signature(x="GeneColorSet", ...)

All additional arguments ... are of the same class as x. The incidence matrix contains elements 0 (genes not present) or 1 (genes present).

signature(x = "GeneSetCollection", ...)

Additional arguments ... can be of class GeneSetCollection or GeneSet. The incidence matrix contains elements 0 (genes not present) or 1 (genes present).

Examples

fl <- system.file("extdata", "Broad.xml", package="GSEABase")
gss <- getBroadSets(fl) # GeneSetCollection of 2 sets
## From one or more GeneSetCollections...
imat <- incidence(gss)
dim(imat)
imat[,c(1:3,ncol(imat)-3+1:3)]

## .. or GeneSets
imat1 <- incidence(gss[[1]], gss[[2]], gss[[1]])
imat1[,1:5]

Bioconductor/GSEABase documentation built on Nov. 2, 2024, 6:35 a.m.