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("ari", "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: ari
for the Adjusted Rand Index, jaccard for the Jaccard Index and
ovlapcoef for the Overlap Coefficient.
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)