mgeneSim {SemSim}R Documentation

Pairwise Semantic Similarity Scores for a Set of Gene Products

Description

Given a set of Entrez Gene IDs, this function returns pairwise semantic similarity or distance scores for all the gene products with GO annotations available.

Usage

mgeneSim(genes, ont = "MF", measure = "Resnik", drop = NULL, db = "all", multiple = "max")

Arguments

genes A set of Entrez Gene IDs.
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 not considered.
db Databases from which the information content has been derived. See description in termSim.
multiple See description in mtermSim.

Value

A matrix of pairwise similarity scores for gene products with GO annotations available.

See Also

geneSim

Examples

  data(Schreiber)
  sim<-mgeneSim(Schreiber, ont="BP", measure="Rel", multiple="rcmax")
  sim[1:3, 1:3]

[Package SemSim version 1.4.0 Index]