update imports from data.table

Author: alexg9010

NAMESPACE

@@ -31,6 +31,7 @@ export(getMethylationStats)
 export(getSampleID)
 export(getTargetAnnotationStats)
 export(getTreatment)
+export(joinSegmentNeighbours)
 export(makeMethylDB)
 export(methRead)
 export(methSeg)
@@ -93,6 +94,7 @@ importFrom(S4Vectors,DataFrame)
 importFrom(S4Vectors,Rle)
 importFrom(S4Vectors,elementMetadata)
 importFrom(S4Vectors,levels)
+importFrom(data.table,":=")
 importFrom(data.table,"key<-")
 importFrom(data.table,CJ)
 importFrom(data.table,SJ)
@@ -107,6 +109,7 @@ importFrom(data.table,setcolorder)
 importFrom(data.table,setkey)
 importFrom(data.table,setkeyv)
 importFrom(data.table,setnames)
+importFrom(data.table,setorder)
 importFrom(data.table,tables)
 importFrom(fastseg,fastseg)
 importFrom(grDevices,colorRamp)

R/methSeg.R

@@ -371,7 +371,7 @@ joinSegmentNeighbours <- function(res) {
 
     ## now we just merge ranges, that had a non-zero value in l
     for (i in which(l!=0)) {
-      res_dt[k[i]:(k[i]+l[i]),`:=`(seqnames=unique(seqnames),
+      res_dt[k[i]:(k[i]+l[i]),":="(seqnames=unique(seqnames),
                                    start=min(start),
                                    end=max(end),
                                    strand = "*",

R/methylKit.R

@@ -11,7 +11,8 @@
 #' 
 #' @importFrom Rsamtools TabixFile scanTabix yieldSize "yieldSize<-"
 #' 
-#' @importFrom data.table data.table fread setnames setcolorder as.data.table tables setkey setkeyv key "key<-" haskey CJ SJ copy rbindlist
+#' @importFrom data.table data.table fread setnames setcolorder as.data.table tables 
+#'             setkey setkeyv key "key<-" haskey CJ SJ copy rbindlist setorder
 #' 
 #' @importFrom mclust  densityMclust Mclust
 #'