geneSim {SemSim}R Documentation

Semantic Similarity Between Two Gene Products

Description

Given two Entrez Gene IDs, this function retrieves GO annotation and calculates their semantic similarity or distance.

Usage

geneSim(gene1, gene2, ont = "MF", measure = "Resnik", drop = NULL, db = "all", multiple = "max")

Arguments

gene1 Entrez Gene ID 1.
gene2 Entrez Gene ID 2.
ont One of "MF", "BP", and "CC" subontologies.
measure One of "Resnik", "Lin", "Rel", and "Jiang" methods.
drop A set of evidence codes based on which certain annotations are dropped.
db Databases from which the information content has been derived. See description in termSim.
multiple Method to be used to combine similarity values if multiple terms are associated with a gene product. See description in mtermSim.

Value

Sim Semantic similarity or distance value.
GO1 Set of terms associated with the first query gene.
GO2 Set of terms associated with the second query gene.

See Also

mtermSim termSim

Examples

  geneSim("852695", "5261")
  geneSim("852695", "5261", ont="BP", measure="Rel", drop=c("IEA", "ISS"), db="human", multiple="rcmax")

[Package SemSim version 1.4.0 Index]