R/getTotalGeneNumber.R

In GeneAnswers: Integrated Interpretation of Genes

`getTotalGeneNumber` <- 
function(categoryType=c('GO', 'GO.BP', 'GO.CC', 'GO.MF', 'DOLITE', 'KEGG', 'REACTOME.PATH'), known=TRUE, annotationLib=c('org.Ag.eg.db', 'org.Bt.eg.db', 'org.Ce.eg.db', 'org.Cf.eg.db', 'org.Dm.eg.db', 
							'org.Dr.eg.db', 'org.EcK12.eg.db', 'org.EcSakai.eg.db', 'org.Gg.eg.db', 'org.Hs.eg.db', 'org.Mm.eg.db', 'org.Mmu.eg.db', 'org.Pt.eg.db', 'org.Rn.eg.db', 
							'org.Ss.eg.db', 'org.Xl.eg.db', 'org.At.tair.db', 'org.Pf.plasmo.db', 'org.Sc.sgd.db')) {
	categoryType <- toupper(categoryType)
	annotationLib <- match.arg(annotationLib) 
	require(annotationLib, character.only=TRUE)
	libname <- sub('\\.db', '', annotationLib)
	idType <- switch(sub('org.*[:.:]', '', libname), 'eg'='EG', 'tair'='TAIR', 'ORF')
	if (!known) return(count.mappedkeys(get(paste(libname, 'GENENAME', sep=''))))
	categoryType <- match.arg(categoryType)
	if (categoryType == 'DOLITE') {
	   if (annotationLib == 'org.Hs.eg.db') return(4051)
	   else stop('DOLite is only designed for human! No data for other species ...')
	}
	
	if (categoryType == 'CABIO.PATH') { 
		stop("Due to termination of caBig, this function is removed in this version!")
#		return(switch(annotationLib,
#			'org.Hs.eg.db'=.getcaBIOIDInfo('http://cabioapi.nci.nih.gov/cabio43/GetXML?query=gov.nih.nci.cabio.domain.Gene&gov.nih.nci.cabio.domain.Pathway[@name=h_*]', IDinfo='geneNumber'), 
#			'org.Mm.eg.db'=.getcaBIOIDInfo('http://cabioapi.nci.nih.gov/cabio43/GetXML?query=gov.nih.nci.cabio.domain.Gene&gov.nih.nci.cabio.domain.Pathway[@name=m_*]', IDinfo='geneNumber'),  
#			NULL))
	}
	
	if (categoryType == 'REACTOME.PATH') {
		species = switch(annotationLib,
			'org.Hs.eg.db'='Homo sapiens: ',
			'org.Mm.eg.db'='Mus musculus: ',
			'org.Rn.eg.db'='Rattus norvegicus: ')
		if (is.null(species)) stop('The current version does not support the given species. Aborting ...')
		# calculate the total gene numbers
		pathways <- toTable(reactomePATHNAME2ID)
		pathwaysSelectedSpecies <- pathways[grep(species, iconv(pathways$path_name)), ]
		return(length(unique(unlist(lookUp(as.character(pathwaysSelectedSpecies[,'DB_ID']), 'reactome', 'PATHID2EXTID')))))
		
#		return(switch(annotationLib,
#			'org.At.tair.db'=2646, 'org.Ce.eg.db'=1909, 'org.Dm.eg.db'=3567, 'org.EcK12.eg.db'=175, 'org.EcSakai.eg.db'=175, 'org.Gg.eg.db'=3108, 'org.Hs.eg.db'=8863, 'org.Mm.eg.db'=5039,  
#			'org.Pf.plasmo.db'=390, 'org.Rn.eg.db'=3809, 'org.Sc.sgd.db'=714, NULL))
	}
	
	return(switch(categoryType,
		'GO' = count.mappedkeys(get(paste(libname, 'GO', sep=''))),
		'KEGG' = count.mappedkeys(get(paste(libname, 'PATH', sep=''))),
		'GO.BP' = length(unique(unlist(lookUp('GO:0008150', libname, paste("GO2ALL", idType, 'S', sep=''))))),
		'GO.MF' = length(unique(unlist(lookUp('GO:0003674', libname, paste("GO2ALL", idType, 'S', sep=''))))),
		'GO.CC' = length(unique(unlist(lookUp('GO:0005575', libname, paste("GO2ALL", idType, 'S', sep=''))))) ))

}