computeMsigOverlap: Compute gene set overlap

In DavisLaboratory/vissE: Visualising Set Enrichment Analysis Results

Compute gene set overlap

Description

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.

Usage

computeMsigOverlap(
  msigGsc1,
  msigGsc2 = NULL,
  thresh = 0.25,
  measure = c("ari", "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: ari for the Adjusted Rand Index, 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)

DavisLaboratory/vissE documentation built on Jan. 31, 2024, 5:02 a.m.