diceSim: Compare pathways

In llrs/BioCor: Functional similarities

Compare pathways

Description

Function to estimate how much two list of genes overlap by looking how much of the nodes are shared. Calculates the Dice similarity

Usage

diceSim(g1, g2)

Arguments

g1, g2

A character list with the names of the proteins in each pathway.

Details

It requires a vector of characters otherwise will return an NA.

Value

A score between 0 and 1 calculated as the double of the proteins shared by g1 and g2 divided by the number of genes in both groups.

Author(s)

Lluís Revilla

See Also

Used for geneSim(), see conversions() help page to transform Dice score to Jaccard score.

Examples

genes.id2 <- c("52", "11342", "80895", "57654", "548953", "11586", "45985")
genes.id1 <- c(
    "52", "11342", "80895", "57654", "58493", "1164", "1163",
    "4150", "2130", "159"
)
diceSim(genes.id1, genes.id2)
diceSim(genes.id2, genes.id2)

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