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")
)

Arguments

msigGsc1

a GeneSetCollection object.

msigGsc2

a GeneSetCollection object or NULL if pairwise overlaps are to be computed.

thresh

a numeric, specifying the threshold to discard pairs of gene sets.

measure

a character, specifying the similarity measure to use: jaccard for the Jaccard Index and ovlapcoef for the Overlap Coefficient.

Value

a data.frame, containing the overlap structure of gene sets represented as a network in the simple interaction format (SIF).

Examples

data(hgsc)
ovlap <- computeMsigOverlap(hgsc)