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### -----------------------------------------------------------------
### Process the direct output from goseq package.
### It outputs the data.frame with indent "."
### -----------------------------------------------------------------
getChildTerms <- function(x, subset, goRelatives, indent="", childEnvir){
result <- character()
if (is.element(x, subset)){
term <- getGOTerm(x)[[1]]
displayLabel <- paste(indent, substr(term, 1, 60), sep="")
result[displayLabel] <- x
## this is the modification to make the table non-redundant!!
subset <- setdiff(subset, x)
}
kids <- intersect(get(x, envir=childEnvir), goRelatives)
indent <- paste(indent, ".")
for (kid in kids){
kidResult <- getChildTerms(kid, subset, goRelatives,
indent=indent, childEnvir)
subset <- setdiff(subset, kidResult)
## again the non-redundancy modification
result <- c(result, kidResult)
}
result
}
### -----------------------------------------------------------------
### make the nice table of GO
### Need to library(GO.db) first
### Not exported!
hierarchicGOTable <- function(x, onto=c("BP", "CC", "MF"),
maxNumberOfTerms=100){
onto <- match.arg(onto)
# x is the output from the goseq pipeline
rownames(x) <- x$category
x <- x[x$ontology==onto, c("over_represented_pvalue", "numDEInCat",
"numInCat", "term", "category")]
colnames(x)[1:3] <- c("Pvalue", "Count", "Size")
if (!is.data.frame(x)){
return(data.frame())
}
if (nrow(x) > maxNumberOfTerms){
x = x[1:maxNumberOfTerms, ]
}
if (nrow(x) == 0){
return(data.frame())
}
if (onto == "CC"){
ANCESTOR <- GOCCANCESTOR
OFFSPRING <- GOCCOFFSPRING
CHILDREN <- GOCCCHILDREN
}
if (onto == "BP"){
ANCESTOR <- GOBPANCESTOR
OFFSPRING <- GOBPOFFSPRING
CHILDREN <- GOBPCHILDREN
}
if (onto == "MF"){
ANCESTOR <- GOMFANCESTOR
OFFSPRING <- GOMFOFFSPRING
CHILDREN <- GOMFCHILDREN
}
goIds <- rownames(x)
goAncestorList <- mget(goIds, envir=ANCESTOR)
goRoots <- character()
for (goId in goIds){
if (length(intersect(goIds, goAncestorList[[goId]])) == 0){
goRoots[goId] <- goId
}
}
goOffsprings <- unique(unlist(mget(goIds, envir=OFFSPRING)))
goAncestors <- unique(unlist(goAncestorList))
goRelatives <- union(intersect(goAncestors, goOffsprings), goIds)
tables <- list()
for (i in 1:length(goRoots)){
childTerms <- getChildTerms(goRoots[i], goIds, goRelatives, indent="",
CHILDREN)
tables[[i]] <-
data.frame(terms=sub("^ ", "", names(childTerms)),
pValues=format(x[childTerms, "Pvalue"], digits=3,
scientific=TRUE),
counts=paste(x[childTerms, "Count"], x[childTerms, "Size"],
sep="/"),
category=x[childTerms, "category"],
stringsAsFactors=FALSE
)
}
ans <- do.call(rbind, tables)
return(ans)
}
## ------------------------------------------------------------------
## Find the closest root of GO terms
## ------------------------------------------------------------------
findGORoot <- function(goIds, onto=c("BP", "CC", "MF")){
onto <- match.arg(onto)
if (onto == "CC"){
ANCESTOR = GOCCANCESTOR
OFFSPRING = GOCCOFFSPRING
CHILDREN = GOCCCHILDREN
}
if (onto == "BP"){
ANCESTOR = GOBPANCESTOR
OFFSPRING = GOBPOFFSPRING
CHILDREN = GOBPCHILDREN
}
if (onto == "MF"){
ANCESTOR = GOMFANCESTOR
OFFSPRING = GOMFOFFSPRING
CHILDREN = GOMFCHILDREN
}
goAncestorList = mget(goIds, envir=ANCESTOR)
goTable <- table(unlist(goAncestorList))
names(goTable)[goTable == length(goAncestorList)]
}
### -----------------------------------------------------------------
### Read the GAF file
### -----------------------------------------------------------------
readGAF <- function(fn){
lines <- readLines(fn)
lines <- lines[-(1:3)]
geneIDs <- sapply(strsplit(lines, "\t"), "[", 2)
GOTerms <- sapply(strsplit(lines, "\t"), "[", 5)
ans <- split(GOTerms, geneIDs)
return(ans)
}
### -----------------------------------------------------------------
### Add ancestor GO
### Exported!
addAncestorGO <- function(go){
if(!is(go, "list")){
stop("`go` must be a list!")
}
goID2Ancestor <- c(as.list(GOBPANCESTOR), as.list(GOMFANCESTOR),
as.list(GOCCANCESTOR))
allGo <- unlist(go)
goID2Ancestor <- lapply(goID2Ancestor, function(x){x[x%in%allGo]})
newGo <- lapply(relist(mapply(append, allGo, goID2Ancestor[allGo]), go),
unlist)
newGo <- lapply(newGo, function(x){if(is.null(x)){character(0)}else{x}})
return(newGo)
}
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