| incidence-methods {GSEABase} | R Documentation |
An incidence matrix summarizes shared membership of gene identifiers across (pairs of) gene sets.
signature(x="GeneSet", ...)
signature(x="GeneColorSet", ...)
... are of the same class as
x. The incidence matrix contains elements 0 (genes not
present) or 1 (genes present).
signature(x = "GeneSetCollection", ...)
... can be of class
GeneSetCollection or GeneSet. The incidence matrix
contains elements 0 (genes not present) or 1 (genes present).
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]