protr (version 1.4-1)

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

Description

This function calculates protein sequence similarity based on Gene Ontology (GO) similarity.

Usage

parGOSim(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', can be one of 'MF', 'BP', or 'CC' subontologies.

organism

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

combine

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

Value

A n x n similarity matrix.

See Also

See twoGOSim for calculating the GO semantic similarity between two groups of GO terms or two Entrez gene IDs. See parSeqSim for paralleled protein similarity calculation based on Smith-Waterman local alignment.

Examples

# NOT RUN {
# Be careful when testing this since it involves GO similarity computation
# and might produce unpredictable results in some environments

library("GOSemSim")
library("org.Hs.eg.db")

# 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 = parGOSim(glist, type = "go", ont = "CC")
print(gsimmat1)

# by Entrez gene id
genelist = list(c("150", "151", "152", "1814", "1815", "1816"))
gsimmat2 = parGOSim(genelist, type = "gene")
print(gsimmat2)
# }