| ... | ... |
@@ -23,11 +23,20 @@ export(writeCombinedEnrichment) |
| 23 | 23 |
import(BiocGenerics) |
| 24 | 24 |
import(IRanges) |
| 25 | 25 |
import(S4Vectors) |
| 26 |
-import(data.table) |
|
| 27 | 26 |
importFrom(GenomicRanges,GRanges) |
| 28 | 27 |
importFrom(GenomicRanges,GRangesList) |
| 29 | 28 |
importFrom(GenomicRanges,elementMetadata) |
| 30 | 29 |
importFrom(GenomicRanges,strand) |
| 30 |
+importFrom(data.table,":=") |
|
| 31 |
+importFrom(data.table,as.data.table) |
|
| 32 |
+importFrom(data.table,data.table) |
|
| 33 |
+importFrom(data.table,fread) |
|
| 34 |
+importFrom(data.table,melt.data.table) |
|
| 35 |
+importFrom(data.table,setDT) |
|
| 36 |
+importFrom(data.table,setcolorder) |
|
| 37 |
+importFrom(data.table,setkey) |
|
| 38 |
+importFrom(data.table,setkeyv) |
|
| 39 |
+importFrom(data.table,setnames) |
|
| 31 | 40 |
importFrom(stats,fisher.test) |
| 32 | 41 |
importFrom(stats,setNames) |
| 33 | 42 |
importFrom(utils,write.table) |
| ... | ... |
@@ -9,8 +9,8 @@ |
| 9 | 9 |
#' |
| 10 | 10 |
#' @references \url{http://github.com/sheffien}
|
| 11 | 11 |
#' @importFrom GenomicRanges GRanges GRangesList elementMetadata strand |
| 12 |
-#' @import BiocGenerics S4Vectors IRanges data.table |
|
| 13 |
-# @importFrom data.table ":=" setDT data.table setkey fread setnames as.data.table setcolorder melt setkeyv |
|
| 12 |
+#' @import BiocGenerics S4Vectors IRanges |
|
| 13 |
+#' @importFrom data.table ":=" setDT data.table setkey fread setnames as.data.table setcolorder melt.data.table setkeyv |
|
| 14 | 14 |
#' @importFrom stats fisher.test setNames |
| 15 | 15 |
#' @importFrom utils write.table |
| 16 | 16 |
NULL |
| ... | ... |
@@ -99,7 +99,7 @@ redefineUserSets=FALSE) {
|
| 99 | 99 |
|
| 100 | 100 |
# To build the fisher matrix, support is 'a' |
| 101 | 101 |
|
| 102 |
- scoreTable = data.table(data.table::melt(t(olmat), variable.factor=FALSE)) |
|
| 102 |
+ scoreTable = data.table(data.table::melt.data.table(t(olmat), variable.factor=FALSE)) |
|
| 103 | 103 |
|
| 104 | 104 |
setnames(scoreTable, c("Var1", "Var2", "value"), c("userSet", "dbSet", "support"))
|
| 105 | 105 |
|
