R/703-calcProtGOSim.R
calcParProtGOSim.Rd
Protein Sequence Similarity Calculation based on Gene Ontology (GO) Similarity
calcParProtGOSim(golist, type = c("go", "gene"), ont = "MF", organism = "human", measure = "Resnik", combine = "BMA")
golist | A character vector, each component contains a character vector of GO terms or one Entrez Gene ID. |
---|---|
type | Input type of |
ont | Default is |
organism | Default is |
measure | Default is |
combine | Default is |
A n
x n
similarity matrix.
This function calculates protein sequence similarity based on Gene Ontology (GO) similarity.
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.
# NOT RUN { # 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) # }# NOT RUN { gsimmat1 = calcParProtGOSim(glist, type = 'go', ont = 'CC') print(gsimmat1) # }# NOT RUN { # by Entrez gene id genelist = list(c('150', '151', '152', '1814', '1815', '1816')) # }# NOT RUN { gsimmat2 = calcParProtGOSim(genelist, type = 'gene') print(gsimmat2) # }