parGOSim {protr} | R Documentation |
Protein Similarity Calculation based on Gene Ontology (GO) Similarity
Description
This function calculates protein similarity based on Gene Ontology (GO) similarity.
Usage
parGOSim(
golist,
type = c("go", "gene"),
ont = c("MF", "BP", "CC"),
organism = "human",
measure = "Resnik",
combine = "BMA"
)
Arguments
golist |
A list, each component contains a character vector of GO terms or one Entrez Gene ID. |
type |
Input type for |
ont |
Default is |
organism |
Organism name. Default is |
measure |
Default is |
combine |
Default is |
Value
A n
x n
similarity matrix.
Author(s)
Nan Xiao <https://nanx.me>
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
# AP4B1
go1 <- c(
"GO:0005215", "GO:0005488", "GO:0005515",
"GO:0005625", "GO:0005802", "GO:0005905"
)
# BCAS2
go2 <- c(
"GO:0005515", "GO:0005634", "GO:0005681",
"GO:0008380", "GO:0031202"
)
# PDE4DIP
go3 <- c(
"GO:0003735", "GO:0005622", "GO:0005840",
"GO:0006412"
)
golist <- list(go1, go2, go3)
parGOSim(golist, type = "go", ont = "CC", measure = "Wang")
# By Entrez gene id
genelist <- list(c("150", "151", "152", "1814", "1815", "1816"))
parGOSim(genelist, type = "gene", ont = "BP", measure = "Wang")
## End(Not run)