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updated call to GOSemSim's goSim function (does not require organism&ontology parameters anymore)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/tRanslatome@121673 bc3139a8-67e5-0310-9ffc-ced21a209358

Erik Dassi authored on 03/10/2016 14:39:17
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@@ -364,8 +364,7 @@ comparisonBetweenTwoLists <- function(go1,go2,ontology,direction) {
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 	for (i in 1:nrow(go1)) {
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 		mat <- NULL
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 		for (j in 1:nrow(go2)) {
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-			sim <- goSim(go1[i, 1], go2[j, 1], 
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-									 organism="human", measure="Wang", ont = ontology)
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+			sim <- goSim(go1[i, 1], go2[j, 1], measure="Wang")
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 			mat <- rbind(mat, c(go1[i, 1],go1[i, 2],go2[j, 1],go2[j, 2],sim))	
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 		}
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