calcParProtGOSim {Rcpi} | R Documentation |
Protein Sequence Similarity Calculation based on Gene Ontology (GO) Similarity
calcParProtGOSim(golist, type = c("go", "gene"), ont = c("MF", "BP", "CC"), 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 |
This function calculates protein sequence similarity based on Gene Ontology (GO) similarity.
A n
x n
similarity matrix.
Nan Xiao <https://nanx.me>
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.
# 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) calcParProtGOSim(glist, type = 'go', ont = 'CC', measure = 'Wang') # By Entrez gene id genelist = list(c('150', '151', '152', '1814', '1815', '1816')) calcParProtGOSim(genelist, type = 'gene', ont = 'BP', measure = 'Wang')