calcTwoProtGOSim {Rcpi} | R Documentation |
Protein Similarity Calculation based on Gene Ontology (GO) Similarity
calcTwoProtGOSim(id1, id2, type = c("go", "gene"), ont = c("MF", "BP", "CC"), 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 |
This function calculates the Gene Ontology (GO) similarity between two groups of GO terms or two Entrez gene IDs.
A n x n matrix.
Nan Xiao <https://nanx.me>
See calcParProtGOSim
for
protein similarity calculation based on
Gene Ontology (GO) semantic similarity.
See calcParProtSeqSim
for paralleled protein similarity
calculation based on sequence alignment.
# By GO terms go1 = c("GO:0004022", "GO:0004024", "GO:0004023") go2 = c("GO:0009055", "GO:0020037") calcTwoProtGOSim(go1, go2, type = 'go', ont = 'MF', measure = 'Wang') # By Entrez gene id gene1 = '241' gene2 = '251' calcTwoProtGOSim(gene1, gene2, type = 'gene', ont = 'CC', measure = 'Lin')