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]