calcTwoProtGOSim {Rcpi} | R Documentation

## Protein Similarity Calculation based on Gene Ontology (GO) Similarity

### Description

Protein Similarity Calculation based on Gene Ontology (GO) Similarity

### Usage

    calcTwoProtGOSim(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 protein.

### Details

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

### Value

A n x n matrix.

### Author(s)

Nan Xiao <https://nanx.me>

### See Also

See `calcParProtGOSim` for protein similarity calculation based on Gene Ontology (GO) semantic similarity. See `calcParProtSeqSim` for paralleled protein similarity calculation based on sequence alignment.

### Examples

    # by GO terms
    go1 = c("GO:0004022", "GO:0004024", "GO:0004023")
    go2 = c("GO:0009055", "GO:0020037")

    gsim1 = calcTwoProtGOSim(go1, go2, type = 'go', ont = 'MF', measure = 'Wang')
    print(gsim1)

    # by Entrez gene id
    gene1 = '241'
    gene2 = '251'

    gsim2 = calcTwoProtGOSim(gene1, gene2, type = 'gene', ont = 'CC', measure = 'Lin')
    print(gsim2)

[Package Rcpi version 1.16.2 Index]