@@ -31,12 +31,12 @@ importFrom(data.table,":=")

 importFrom(data.table,as.data.table)

 importFrom(data.table,data.table)

 importFrom(data.table,fread)

-importFrom(data.table,melt.data.table)

 importFrom(data.table,setDT)

 importFrom(data.table,setcolorder)

 importFrom(data.table,setkey)

 importFrom(data.table,setkeyv)

 importFrom(data.table,setnames)

+importFrom(reshape2,melt)

 importFrom(stats,fisher.test)

 importFrom(stats,setNames)

 importFrom(utils,write.table)

@@ -10,7 +10,8 @@

 #' @references \url{http://github.com/sheffien}

 #' @importFrom GenomicRanges GRanges GRangesList elementMetadata strand

 #' @import BiocGenerics S4Vectors IRanges

-#' @importFrom data.table ":=" setDT data.table setkey fread setnames as.data.table setcolorder melt.data.table setkeyv

+#' @importFrom reshape2 melt

+#' @importFrom data.table ":=" setDT data.table setkey fread setnames as.data.table setcolorder setkeyv

 #' @importFrom stats fisher.test setNames

 #' @importFrom utils write.table

 NULL

@@ -84,7 +84,6 @@ redefineUserSets=FALSE) {

 	# dbSets (rows) by userSets (columns), counting overlap.

 	olmat = do.call(cbind, geneSetDatabaseOverlap)

-

 	message("Calculating universe set overlaps...")

 	# Now for each test set, how many items *in the universe* does

 	# it overlap? This will go into the calculation for c

@@ -99,7 +98,7 @@ redefineUserSets=FALSE) {

 	# To build the fisher matrix, support is 'a'

-	scoreTable = data.table(data.table::melt.data.table(t(olmat), variable.factor=FALSE))

+	scoreTable = data.table(reshape2::melt(t(olmat), variable.factor=FALSE))

 	setnames(scoreTable, c("Var1", "Var2", "value"), c("userSet", "dbSet", "support"))