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##Copyright R. Gentleman, 2004
##simple functions to get Evidence codes
.isMissingGOEntry <- function(x) (length(x) == 1L && is.na(x))
##get then GO term names for a particular (sub)ontology
getOntology = function(inlist, ontology=c("MF", "BP", "CC")) {
which = match.arg(ontology)
onts = sapply(inlist, function(z) {
if (!.isMissingGOEntry(z))
z$Ontology
else
z
})
onts = onts[!is.na(onts)]
unique(names(inlist[onts %in% which]))
}
##get GO evidence codes
getEvidence = function(inlist) {
ans <- sapply(inlist, function(z) {
if (!.isMissingGOEntry(z))
z$Evidence
else
z
})
ans[!is.na(ans)]
}
##drop a specified set of evidence codes
dropECode = function(inlist, code = "IEA") {
hasCode = sapply(inlist, function(z) {
if (!.isMissingGOEntry(z))
z$Evidence
else
z
})
hasCode <- hasCode[!is.na(hasCode)]
badVals = hasCode %in% code
inlist[!badVals]
}
## helper function, determines if there is a GO annotation for the
## desired mode
hasGOannote <- function(x, which="MF") {
if (is(x, "GOTerms")) {
cat <- Ontology(x)
if (!is.na(cat) && cat == which)
return(TRUE) else return(FALSE)
}
if (is.list(x)) {
gT <- sapply(x, function(y) is(y, "GOTerms"))
if (any(gT)) {
if (all(gT)) {
cats <- sapply(x, Ontology)
return(cats == which)
}
else
stop("mixed arguments not allowed")
}
}
if (!is.character(x))
stop("wrong argument")
tm <- getGOOntology(x)
return(tm == which)
}
##three functions to get all the GO information for a set of GO terms
##FIXME: these need to be renovated - probably removed even..
getGOOntology <- function(x) {
if( !is.character(x) )
stop("need a character argument")
if(length(x) == 0 )
return( character(0))
loadNamespace("GO.db")
wh <- mget(x, envir=GO.db::GOTERM, ifnotfound=NA)
return( sapply(wh, Ontology) )
}
getGOParents <- function(x) {
if( !is.character(x) )
stop("need a character argument")
if(length(x) == 0 )
return(list())
loadNamespace("GO.db")
MF_parents <- mget(x, envir=GO.db::GOMFPARENTS, ifnotfound=NA)
BP_parents <- mget(x, envir=GO.db::GOBPPARENTS, ifnotfound=NA)
CC_parents <- mget(x, envir=GO.db::GOCCPARENTS, ifnotfound=NA)
lapply(setNames(seq_along(x), x),
function(i) {
xi_parents <- MF_parents[[i]]
if (!identical(xi_parents, NA))
return(list(Ontology="MF", Parents=xi_parents))
xi_parents <- BP_parents[[i]]
if (!identical(xi_parents, NA))
return(list(Ontology="BP", Parents=xi_parents))
xi_parents <- CC_parents[[i]]
if (!identical(xi_parents, NA))
return(list(Ontology="CC", Parents=xi_parents))
stop(paste(x[[i]], "is not a member of any ontology"))
}
)
}
getGOChildren <- function(x) {
if( !is.character(x) )
stop("need a character argument")
if(length(x) == 0 )
return(list())
loadNamespace("GO.db")
MF_children <- mget(x, envir=GO.db::GOMFCHILDREN, ifnotfound=NA)
BP_children <- mget(x, envir=GO.db::GOBPCHILDREN, ifnotfound=NA)
CC_children <- mget(x, envir=GO.db::GOCCCHILDREN, ifnotfound=NA)
lapply(setNames(seq_along(x), x),
function(i) {
xi_children <- MF_children[[i]]
if (!identical(xi_children, NA))
return(list(Ontology="MF", Children=xi_children))
xi_children <- BP_children[[i]]
if (!identical(xi_children, NA))
return(list(Ontology="BP", Children=xi_children))
xi_children <- CC_children[[i]]
if (!identical(xi_children, NA))
return(list(Ontology="CC", Children=xi_children))
list() # not an error (unlike for getGOParents() above)
}
)
}
getGOTerm <- function(x) {
if( !is.character(x) )
stop("need a character argument")
if(length(x) == 0 )
return(list())
loadNamespace("GO.db")
terms <- mget(x, envir=GO.db::GOTERM, ifnotfound=NA)
isNA = sapply(terms,function(x) !(isS4(x) && is(x, "GOTerms")))
if( any(isNA) )
terms = terms[!isNA]
ontology <- sapply(terms, Ontology)
terms = sapply(terms, Term)
return(split(terms, ontology))
}
filterGOByOntology <- function(goids, ontology=c("BP", "CC", "MF")) {
ontology <- match.arg(ontology)
eName <- switch(ontology,
BP="GOBPPARENTS",
CC="GOCCPARENTS",
MF="GOMFPARENTS",
stop("invalid ontology ", ontology))
e <- get(eName)
goids %in% ls(e)
}
aqListGOIDs <- function(ont) {
## Return all GO IDs in the specified ontologies
ont <- unique(ont)
knownOnts <- c("BP", "CC", "MF")
badOnt <- ont[!(ont %in% knownOnts)]
if (length(badOnt))
stop("Unknown ontology codes: ", paste(badOnt, collapse=", "),
"\nvalid codes are: ", paste(knownOnts, collapse=", "))
## determine size
lens <- integer(length(ont))
for (i in seq(along=ont))
lens[i] <- length(getAnnMap(paste(ont[i], "PARENTS", sep=""),
chip="GO"))
## retrieve IDs
ans <- character(sum(lens))
lens <- c(0L, lens)
for (i in seq(along=ont)) {
ans[lens[i]+1:lens[i+1]] <- ls(getAnnMap(paste(ont[i], "PARENTS", sep=""),
chip="GO"))
}
ans
}
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