incidence-methods {GSEABase} | R Documentation |
An incidence matrix summarizes shared membership of gene identifiers across (pairs of) gene sets.
signature(x = "GeneColor", ...)
...
are GeneColor
sets. The
incidence matrix is 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]