add tile,GenomicRanges

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@84129 bc3139a8-67e5-0310-9ffc-ced21a209358
RamsinghLab · Dec 10, 2013 · adee2e2 · adee2e2
1 parent ecd4590
commit adee2e2
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Showing 3 changed files with 18 additions and 3 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -7,12 +7,12 @@ Description: The ability to efficiently represent and manipulate genomic
 	intervals. Specialized containers for representating and manipulating
 	short alignments against a reference genome are defined in the
 	GenomicAlignments package.
-Version: 1.15.12
+Version: 1.15.13
 Author: P. Aboyoun, H. Pages and M. Lawrence
 Maintainer: Bioconductor Package Maintainer <[email protected]>
 biocViews: Genetics, Sequencing, HighThroughputSequencing, Annotation
 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.7.7),
-	IRanges (>= 1.21.13), XVector (>= 0.3.2)
+	IRanges (>= 1.21.14), XVector (>= 0.3.2)
 Imports: methods, utils, stats, BiocGenerics, IRanges
 LinkingTo: IRanges, XVector
 Suggests: AnnotationDbi (>= 1.21.1), AnnotationHub,

diff --git a/NAMESPACE b/NAMESPACE
@@ -74,7 +74,8 @@ exportMethods(
     findOverlaps, countOverlaps, overlapsAny, subsetByOverlaps,
     precede, follow, nearest, distance, distanceToNearest,
     map,
-    encodeOverlaps
+    encodeOverlaps,
+    tile
 )
 
 

diff --git a/R/tile-methods.R b/R/tile-methods.R
@@ -0,0 +1,14 @@
+### =========================================================================
+### "tile" methods
+### -------------------------------------------------------------------------
+###
+
+setMethod("tile", "GenomicRanges", function(x, n, width) {
+  sn <- seqnames(x)
+  strand <- strand(x)
+  x <- ranges(x)
+  tiles <- callGeneric()
+  gr <- GRanges(rep(sn, elementLengths(tiles)), unlist(tiles),
+                rep(strand, elementLengths(tiles)))
+  relist(gr, tiles)
+})