pathSim: Calculates the Dice similarity between pathways

In llrs/BioCor: Functional similarities

Calculates the Dice similarity between pathways

Description

Calculates the similarity between pathways using dice similarity score. diceSim is used to calculate similarities between the two pathways.

Usage

pathSim(pathway1, pathway2, info)

## S4 method for signature 'character,character,GeneSetCollection'
pathSim(pathway1, pathway2, info)

Arguments

pathway1, pathway2	A single pathway to calculate the similarity
info	A GeneSetCollection or a list of genes and the pathways they are involved.

Value

The similarity between those pathways or all the similarities between each comparison.

Methods (by class)

• pathSim(pathway1 = character, pathway2 = character, info = GeneSetCollection): Calculates all the similarities of a GeneSetCollection and combine them using combineScoresPar

Author(s)

Lluís Revilla

See Also

conversions() help page to transform Dice score to Jaccard score. mpathSim() for multiple pairwise comparison of pathways.

Examples

if (require("reactome.db")) {
    # Extracts the paths of all genes of org.Hs.eg.db from reactome
    genes.react <- as.list(reactomeEXTID2PATHID)
    (paths <- sample(unique(unlist(genes.react)), 2))
    pathSim(paths[1], paths[2], genes.react)
} else {
    warning("You need reactome.db package for this example")
}

llrs/BioCor documentation built on April 24, 2024, 5:50 p.m.