Compare pathways — diceSim • BioCor

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.

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.

Details

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

See also

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

Author

Lluís Revilla

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)
#> [1] 0.4705882
diceSim(genes.id2, genes.id2)
#> [1] 1