Nothing
ovreGO <- function(genes, allgenes, ontology="BP", algorithm="parentchild", statistic="fisher", map="org.Hs.eg.db", nterm=100, plot=FALSE, nword=30, min.freq=1, scale=c(2,0.5), ...){
geneList <- factor(as.integer(allgenes %in% genes))
names(geneList) <- allgenes
godata <- new("topGOdata", ontology=ontology, allGenes=geneList, annot = annFUN.org, mapping=map)
result <- runTest(godata, algorithm = algorithm, statistic = statistic)
orGO <- GenTable(godata, result, topNodes=nterm)
lc <- unlist(mget(orGO$GO.ID, LC, ifnotfound=NA))
pv <- score(result)
pv <- pv[match(orGO$GO.ID, names(pv))]
#lc <- unlist(mget(orGO$GO.ID, LC))
Score <- -log10(pv)
wScore <- Score * lc
wScore[is.na(wScore)] <- 0
orGO <- cbind(orGO, Score, wScore)
if(plot==TRUE){
words <- Term(as.character(orGO$GO.ID))
wn <- nchar(words)
words[wn>nword] <- substr(words[wn>nword], start=1, stop=nword-2)
words[wn>nword] <- paste(words[wn>nword],"..",sep="")
colors <- brewer.pal(8,"Dark2")
wordcloud(words, freq=round(orGO[,"wScore"]), min.freq=min.freq, scale=scale, colors=colors, ...)
}
orGO
}
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