parGOSim {rDNAse} | R Documentation |
DNA Sequence Similarity Calculation based on Gene Ontology (GO) Similarity
Description
DNA Sequence Similarity Calculation 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 |
ont |
Default is |
organism |
Default is |
measure |
Default is |
combine |
Default is |
Details
This function calculates DNA sequence similarity based on Gene Ontology (GO) similarity.
Value
A n
x n
similarity matrix.
Author(s)
Min-feng Zhu <wind2zhu@163.com>
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 DNA 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
require(GOSemSim)
require(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)
## End(Not run)