Compute overlap between gene sets from a GeneSetCollection using the Jaccard index or the overlap coefficient. These values can then be used to compute a network of gene set overlaps.
computeMsigOverlap( msigGsc1, msigGsc2 = NULL, thresh = 0.25, measure = c("jaccard", "ovlapcoef") )
a GeneSetCollection object.
a GeneSetCollection object or NULL if pairwise overlaps are to be computed.
a numeric, specifying the threshold to discard pairs of gene sets.
a character, specifying the similarity measure to use:
jaccard for the Jaccard Index and
ovlapcoef for the Overlap
a data.frame, containing the overlap structure of gene sets represented as a network in the simple interaction format (SIF).
data(hgsc) ovlap <- computeMsigOverlap(hgsc)