rDNAse (version 1.1-1)

parGOSim: 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 golist, 'go' for GO Terms, 'gene' for gene ID.

ont

Default is 'MF', could be one of 'MF', 'BP', or 'CC' subontologies.

organism

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

combine

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

Value

A n x n similarity matrix.

Details

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

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)