R/703-calcProtGOSim.R
calcTwoProtGOSim.Rd
Protein Similarity Calculation based on Gene Ontology (GO) Similarity
calcTwoProtGOSim(id1, id2, type = c("go", "gene"), ont = "MF", organism = "human", measure = "Resnik", combine = "BMA")
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, |
ont | Default is |
organism | Default is |
measure | Default is |
combine | Default is |
A n x n matrix.
This function calculates the Gene Ontology (GO) similarity between two groups of GO terms or two Entrez gene IDs.
See calcParProtGOSim
for
protein similarity calculation based on
Gene Ontology (GO) semantic similarity.
See calcParProtSeqSim
for paralleled protein similarity
calculation based on sequence alignment.
# NOT RUN { # by GO terms go1 = c("GO:0004022", "GO:0004024", "GO:0004023") go2 = c("GO:0009055", "GO:0020037") # }# NOT RUN { gsim1 = calcTwoProtGOSim(go1, go2, type = 'go', ont = 'MF', measure = 'Wang') print(gsim1) # }# NOT RUN { # by Entrez gene id gene1 = '241' gene2 = '251' # }# NOT RUN { gsim2 = calcTwoProtGOSim(gene1, gene2, type = 'gene', ont = 'CC', measure = 'Lin') print(gsim2) # }