twoGOSim: DNA Similarity Calculation based on Gene Ontology (GO) Similarity

Description

DNA Similarity Calculation based on Gene Ontology (GO) Similarity

Usage

twoGOSim(id1, id2, type = c("go", "gene"), ont = "MF", organism = "human", measure = "Resnik", combine = "BMA")

Arguments

id1

A character vector. length > 1: each element is a GO term; length = 1: the Entrez Gene ID.

id2

A character vector. length > 1: each element is a GO term; length = 1: the Entrez Gene ID.

type

Input type of id1 and id2, 'go' for GO Terms, 'gene' for gene ID.

ont

Default is 'MF', could be one of 'MF', 'BP', or 'CC' subontologies.

organism

Default is 'human', could be one of 'anopheles', 'arabidopsis', 'bovine', 'canine', 'chicken', 'chimp', 'coelicolor', 'ecolik12', 'ecsakai', 'fly', 'human', 'malaria', 'mouse', 'pig', 'rat', 'rhesus', 'worm', 'xenopus', 'yeast' or 'zebrafish'.

measure

Default is 'Resnik', could be one of 'Resnik', 'Lin', 'Rel', 'Jiang' or 'Wang'.

combine

Default is 'BMA', could be one of 'max', 'average', 'rcmax' or 'BMA' for combining semantic similarity scores of multiple GO terms associated with DNA.

Value

A n x n matrix.

Details

This function calculates the Gene Ontology (GO) similarity between two groups of GO terms or two Entrez gene IDs.

Examples

Run this code

## Not run: 
# # Be careful when testing this since it involves GO similarity computation
# # and might produce unpredictable results in some environments
# 
# require(GOSemSim)
# require(org.Hs.eg.db)
# 
# # by GO terms
# go1 = c("GO:0004022", "GO:0004024", "GO:0004023")
# go2 = c("GO:0009055", "GO:0020037")
# gsim1 = twoGOSim(go1, go2, type = 'go', ont = 'MF', measure = 'Wang')
# print(gsim1)
# 
# # by Entrez gene id
# gene1 = '241'
# gene2 = '251'
# gsim2 = twoGOSim(gene1, gene2, type = 'gene', ont = 'BP', measure = 'Lin')
# print(gsim2)## End(Not run)