Nothing
# getMGTerms # used by createHTML y getTerms
# clDescriptions # used by getMGTerms
# Returns a list with the metagroup term names and links
getMGTerms <- function(globalMetagroups, grType)
{
mgTerms<- sapply(globalMetagroups$Terms, function(x) strsplit(as.character(x), split=";"))
names(mgTerms)<-paste(grType,rownames(globalMetagroups), sep=" ")
termsDescriptions <- list()
for(mgName in names(mgTerms))
{
descripciones <- clDescriptions(mgTerms[[mgName]])
descripciones <- descripciones[order(descripciones[,"TermDescription"]),, drop=FALSE]
termsDescriptions[[mgName]] <- descripciones
}
return(termsDescriptions)
}
clDescriptions <- function(terms) #org=NULL,
{
termsIDs <- regexpr("\\(([[:alnum:]]+:[[:alnum:]]+[0-9]+)\\)$", terms)
termsIDs <- substr(terms, termsIDs + 1, termsIDs + attr(termsIDs, "match.length") - 2)
termsTable <- cbind(Term=terms, TermID=termsIDs)
rownames(termsTable) <- termsTable[,"Term"]
termsTable <- cbind(termsTable[,"TermID",drop=FALSE], TermDescription= apply(termsTable, 1, function(x) gsub(paste(" (",x[2],")",sep=""),"", x[1], fixed=TRUE)))
termsTable <- cbind(termsTable, Annotation=sapply(strsplit(termsTable[,"TermID"],":", fixed=TRUE), function(x) x[1]))
# Get term links
if(all(termsTable[,"TermID"]==""))
{
links <- rep(NA, length(termsTable[,"TermID"]))
}else
{
links <- sapply(sapply(termsTable[,"TermID"], function(y) strsplit(y, split=":")), function(x)
{
# Link (Only for Kegg and Interpro)
link <- NA
if(length(x)>0)
{
# Interpro
# David: IPR:000719:Protein kinase, core
# gtLinker: IPR:000980:SH2 motif
if(toupper(x[1])=="IPR") # TO DO REVISAR!!! NEW VERSION!!
{
link <- paste("http://www.ebi.ac.uk/interpro/entry/IPR", x[2], sep="")
}
# # Kegg
# if(toupper(x[1])=="KEGG")
# {
# # KEGG:hsa03320:PPAR signaling pathway
# org <- substring(x[2], 1, 3)
# keggID <- substring(x[2], 4, nchar(x[2]))
# if(keggID %in% names(keggPlots))
# {
# link <- keggPlots[keggID]
# }else
# {
# link <- paste("http://www.genome.jp/kegg-bin/show_pathway?org_name=", org, "&mapno=", keggID, sep="")
# }
# }
# SMART (Appears in david even if it was not explicitly requested)
# David: SM00181:EGF
if(toupper(x[1])=="SM0") link <- paste("http://smart.embl.de/smart/do_annotation.pl?DOMAIN=", x[1], sep="")
# REACTOME
if(toupper(x[1])=="REACT") link <- paste("http://www.reactome.org/content/detail/", x[2], sep="")
}
return (link)
})
}
termsTable <- cbind(termsTable, Link=links)
return(termsTable)
}
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