geneSets.sim: Compute the similarities between a collection of gene sets.

In massiveGST: Competitive Gene Sets Test with the Mann-Whitney-Wilcoxon Test

Compute the similarities between a collection of gene sets.

Description

Compute the similarities between a collection of gene sets using a convex function of the Jaccard and overlap indeces.

Usage

geneSets.sim(gs, eps = 0.25)

Arguments

gs	a character vector of gene-sets.
eps	a real value between 0.0 and 1.0 controlling the contribution of the Jaccard and overlap similaties to their convex combination; eps = 0.25 (default), see details.

Details

The similarity between the gene-set is computed a convex combination of the Jaccard and overlap similarities. See the reference for further details.

Value

returns an object of class "dist", where the values are the similaties between gene sets.

Author(s)

Stefano M. Pagnotta

References

Cerulo, Pagnotta (2022) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.3390/e24050739")}

See Also

dist

Examples

library(massiveGST)

# get the gene-sets
fname <- system.file("extdata", package="massiveGST")
fname <- file.path(fname, "h.all.v2024.1.Hs.symbols.gmt")
geneSets <- get_geneSets_from_local_files(fname)[1:5]

# compute the similarities
geneSets.sim(geneSets)
ssim <- geneSets.sim(geneSets)
ssim <- as.matrix(ssim)
diag(ssim) <- 1
ssim

massiveGST documentation built on April 3, 2025, 10:57 p.m.