calcParProtGOSim {Rcpi} | R Documentation

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

### Description

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

### Usage

    calcParProtGOSim(golist, type = c("go", "gene"), ont = "MF",
      organism = "human", measure = "Resnik", combine = "BMA")

### Arguments

`golist` | A character vector, each component contains a character vector of GO terms or one Entrez Gene ID.
`type` | Input type of `golist`, `'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 protein sequence similarity based on Gene Ontology (GO) similarity.

### Value

A `n` x `n` similarity matrix.

### Author(s)

Nan Xiao <https://nanx.me>

### See Also

See `calcTwoProtGOSim` for calculating the GO semantic similarity between two groups of GO terms or two Entrez gene IDs. See `calcParProtSeqSim` for paralleled protein similarity calculation based on sequence alignment.

### Examples

    # by GO Terms
    go1 = c('GO:0005215', 'GO:0005488', 'GO:0005515', 'GO:0005625', 'GO:0005802', 'GO:0005905')  # AP4B1
    go2 = c('GO:0005515', 'GO:0005634', 'GO:0005681', 'GO:0008380', 'GO:0031202')  # BCAS2
    go3 = c('GO:0003735', 'GO:0005622', 'GO:0005840', 'GO:0006412')  # PDE4DIP
    glist = list(go1, go2, go3)

    gsimmat1 = calcParProtGOSim(glist, type = 'go', ont = 'CC')
    print(gsimmat1)

    # by Entrez gene id
    genelist = list(c('150', '151', '152', '1814', '1815', '1816'))

    gsimmat2 = calcParProtGOSim(genelist, type = 'gene')
    print(gsimmat2)

[Package Rcpi version 1.16.2 Index]