- Add 'algorithm' arg to usage section.

- Fix GIntervalTree broken example.
- Other minor tweaks.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@97360 bc3139a8-67e5-0310-9ffc-ced21a209358

R/findOverlaps-GIntervalTree-methods.R

@@ -85,3 +85,7 @@ setMethod("findOverlaps", c("GenomicRanges", "GIntervalTree"),
     Hits(q_hits, s_hits, q_len, s_len)
 })
 
+setMethod("countOverlaps", c("GenomicRanges", "GIntervalTree"),
+    countOverlaps.definition
+)
+

R/nearest-methods.R

@@ -46,7 +46,8 @@
                   queryLength=as.integer(max(c(0, queryHits))),
                   subjectLength=as.integer(max(c(0, subjectHits))))
 {
-    Hits(queryHits, subjectHits, queryLength, subjectLength)
+    o <- S4Vectors:::orderIntegerPairs(queryHits, subjectHits)
+    Hits(queryHits[o], subjectHits[o], queryLength, subjectLength)
 }
 
 .findPrecedeFollow_pmin <-

man/GIntervalTree-class.Rd

@@ -35,7 +35,7 @@
 \title{GIntervalTree objects}
 
 \description{
-  The GRanges class is a container for the genomic locations and
+  The GIntervalTree class is a container for the genomic locations and
   their associated annotations.
 }
 

man/GRanges-class.Rd

@@ -58,7 +58,6 @@
 \alias{[,List,GenomicRanges-method}
 \alias{[,list,GenomicRanges-method}
 \alias{c,GenomicRanges-method}
-\alias{tile,GenomicRanges-method}
 \alias{window,GenomicRanges-method}
 
 % $ and $<- methods:
@@ -331,15 +330,6 @@
       elements are removed from the returned object if \code{drop} is
       \code{TRUE}.
     }
-    \item{}{
-      \code{tile(x, n, width)}: Splits \code{x} into a
-      \code{GRangesList}, each element of which corresponds to a tile,
-      or partition, of \code{x}. Specify the tile geometry with either
-      \code{n} or \code{width} (not both). Passing \code{n} creates
-      \code{n} tiles of approximately equal width, truncated by sequence
-      end, while passing \code{width} tiles the region with ranges of
-      the given width, again truncated by sequence end.
-    }
   }
 }
 

man/findOverlaps-methods.Rd

@@ -20,6 +20,7 @@
 \alias{countOverlaps,GenomicRanges,Vector-method}
 \alias{countOverlaps,Vector,GenomicRanges-method}
 \alias{countOverlaps,GenomicRanges,GenomicRanges-method}
+\alias{countOverlaps,GenomicRanges,GIntervalTree-method}
 \alias{countOverlaps,GRangesList,Vector-method}
 \alias{countOverlaps,Vector,GRangesList-method}
 \alias{countOverlaps,GRangesList,GRangesList-method}
@@ -72,25 +73,29 @@
 
 \usage{
 \S4method{findOverlaps}{GenomicRanges,GenomicRanges}(query, subject,
-    maxgap = 0L, minoverlap = 1L,
-    type = c("any", "start", "end", "within", "equal"),
-    select = c("all", "first", "last", "arbitrary"),
-    ignore.strand = FALSE)
+    maxgap=0L, minoverlap=1L,
+    type=c("any", "start", "end", "within", "equal"),
+    select=c("all", "first", "last", "arbitrary"),
+    algorithm=c("nclist", "intervaltree"),
+    ignore.strand=FALSE)
 
 \S4method{countOverlaps}{GenomicRanges,GenomicRanges}(query, subject,
-    maxgap = 0L, minoverlap = 1L,
-    type = c("any", "start", "end", "within", "equal"), 
-    ignore.strand = FALSE)
+    maxgap=0L, minoverlap=1L,
+    type=c("any", "start", "end", "within", "equal"),
+    algorithm=c("nclist", "intervaltree"),
+    ignore.strand=FALSE)
 
 \S4method{overlapsAny}{GenomicRanges,GenomicRanges}(query, subject,
-    maxgap = 0L, minoverlap = 1L,
-    type = c("any", "start", "end", "within", "equal"), 
-    ignore.strand = FALSE)
+    maxgap=0L, minoverlap=1L,
+    type=c("any", "start", "end", "within", "equal"),
+    algorithm=c("nclist", "intervaltree"),
+    ignore.strand=FALSE)
 
 \S4method{subsetByOverlaps}{GenomicRanges,GenomicRanges}(query, subject,
-    maxgap = 0L, minoverlap = 1L,
-    type = c("any", "start", "end", "within", "equal"),
-    ignore.strand = FALSE)
+    maxgap=0L, minoverlap=1L,
+    type=c("any", "start", "end", "within", "equal"),
+    algorithm=c("nclist", "intervaltree"),
+    ignore.strand=FALSE)
 }
 
 \arguments{
@@ -141,7 +146,7 @@
 
 \value{
   For \code{findOverlaps} either a \link[S4Vectors]{Hits} object when
-  \code{select = "all"} or an integer vector otherwise. 
+  \code{select="all"} or an integer vector otherwise. 
 
   For \code{countOverlaps} an integer vector containing the tabulated
   query overlap hits.
@@ -174,49 +179,43 @@
 
 \examples{
 ## GRanges object:
-gr <-
-  GRanges(seqnames =
-          Rle(c("chr1", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)),
-          ranges =
-          IRanges(1:10, width = 10:1, names = head(letters,10)),
-          strand =
-          Rle(strand(c("-", "+", "*", "+", "-")),
-              c(1, 2, 2, 3, 2)),
-          score = 1:10,
-          GC = seq(1, 0, length=10))
+gr <- GRanges(
+        seqnames=Rle(c("chr1", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)),
+        ranges=IRanges(1:10, width=10:1, names=head(letters,10)),
+        strand=Rle(strand(c("-", "+", "*", "+", "-")), c(1, 2, 2, 3, 2)),
+        score=1:10,
+        GC=seq(1, 0, length=10)
+      )
 gr
 
 ## GRangesList object:
-gr1 <-
-  GRanges(seqnames = "chr2", ranges = IRanges(4:3, 6),
-          strand = "+", score = 5:4, GC = 0.45)
-gr2 <-
-  GRanges(seqnames = c("chr1", "chr1"),
-          ranges = IRanges(c(7,13), width = 3),
-          strand = c("+", "-"), score = 3:4, GC = c(0.3, 0.5))
-gr3 <-
-  GRanges(seqnames = c("chr1", "chr2"),
-          ranges = IRanges(c(1, 4), c(3, 9)),
-          strand = c("-", "-"), score = c(6L, 2L), GC = c(0.4, 0.1))
-grl <- GRangesList("gr1" = gr1, "gr2" = gr2, "gr3" = gr3)
+gr1 <- GRanges(seqnames="chr2", ranges=IRanges(4:3, 6),
+               strand="+", score=5:4, GC=0.45)
+gr2 <- GRanges(seqnames=c("chr1", "chr1"),
+               ranges=IRanges(c(7,13), width=3),
+               strand=c("+", "-"), score=3:4, GC=c(0.3, 0.5))
+gr3 <- GRanges(seqnames=c("chr1", "chr2"),
+               ranges=IRanges(c(1, 4), c(3, 9)),
+               strand=c("-", "-"), score=c(6L, 2L), GC=c(0.4, 0.1))
+grl <- GRangesList("gr1"=gr1, "gr2"=gr2, "gr3"=gr3)
 
 ## Overlapping two GRanges objects:
 table(!is.na(findOverlaps(gr, gr1, select="arbitrary")))
 countOverlaps(gr, gr1)
 findOverlaps(gr, gr1)
 subsetByOverlaps(gr, gr1)
 
-countOverlaps(gr, gr1, type = "start")
-findOverlaps(gr, gr1, type = "start")
-subsetByOverlaps(gr, gr1, type = "start")
+countOverlaps(gr, gr1, type="start")
+findOverlaps(gr, gr1, type="start")
+subsetByOverlaps(gr, gr1, type="start")
 
-findOverlaps(gr, gr1, select = "first")
-findOverlaps(gr, gr1, select = "last")
+findOverlaps(gr, gr1, select="first")
+findOverlaps(gr, gr1, select="last")
 
 findOverlaps(gr1, gr)
-findOverlaps(gr1, gr, type = "start")
-findOverlaps(gr1, gr, type = "within")
-findOverlaps(gr1, gr, type = "equal")
+findOverlaps(gr1, gr, type="start")
+findOverlaps(gr1, gr, type="within")
+findOverlaps(gr1, gr, type="equal")
 
 ## using a GIntervalTree
 gtree <- GIntervalTree(gr1)
@@ -230,20 +229,20 @@ table(!is.na(findOverlaps(grl, gr, select="first")))
 countOverlaps(grl, gr)
 findOverlaps(grl, gr)
 subsetByOverlaps(grl, gr)
-countOverlaps(grl, gr, type = "start")
-findOverlaps(grl, gr, type = "start")
-subsetByOverlaps(grl, gr, type = "start")
-findOverlaps(grl, gr, select = "first")
+countOverlaps(grl, gr, type="start")
+findOverlaps(grl, gr, type="start")
+subsetByOverlaps(grl, gr, type="start")
+findOverlaps(grl, gr, select="first")
 
 ## using a GIntervalTree
 table(!is.na(findOverlaps(grl, gtree, select="first")))
 countOverlaps(grl, gtree)
 findOverlaps(grl, gtree)
 subsetByOverlaps(grl, gtree)
-countOverlaps(grl, gtree, type = "start")
-findOverlaps(grl, gtree, type = "start")
-subsetByOverlaps(grl, gtree, type = "start")
-findOverlaps(grl, gtree, select = "first")
+countOverlaps(grl, gtree, type="start")
+findOverlaps(grl, gtree, type="start")
+subsetByOverlaps(grl, gtree, type="start")
+findOverlaps(grl, gtree, select="first")
 
 ## Overlapping two GRangesList objects:
 countOverlaps(grl, rev(grl))

man/nearest-methods.Rd

@@ -21,14 +21,14 @@
 }
 
 \usage{
-\S4method{precede}{GenomicRanges,GenomicRanges}(x, subject, select=c("arbitrary", "all"), ignore.strand=FALSE, ...)
-\S4method{precede}{GenomicRanges,missing}(x, subject, select=c("arbitrary", "all"), ignore.strand=FALSE, ...)
+\S4method{precede}{GenomicRanges,GenomicRanges}(x, subject, select=c("arbitrary", "all"), ignore.strand=FALSE)
+\S4method{precede}{GenomicRanges,missing}(x, subject, select=c("arbitrary", "all"), ignore.strand=FALSE)
 
-\S4method{follow}{GenomicRanges,GenomicRanges}(x, subject, select=c("arbitrary", "all"), ignore.strand=FALSE, ...)
-\S4method{follow}{GenomicRanges,missing}(x, subject, select=c("arbitrary", "all"), ignore.strand=FALSE, ...)
+\S4method{follow}{GenomicRanges,GenomicRanges}(x, subject, select=c("arbitrary", "all"), ignore.strand=FALSE)
+\S4method{follow}{GenomicRanges,missing}(x, subject, select=c("arbitrary", "all"), ignore.strand=FALSE)
 
-\S4method{nearest}{GenomicRanges,GenomicRanges}(x, subject, select=c("arbitrary", "all"), ignore.strand=FALSE, ...)
-\S4method{nearest}{GenomicRanges,missing}(x, subject, select=c("arbitrary", "all"), ignore.strand=FALSE, ...)
+\S4method{nearest}{GenomicRanges,GenomicRanges}(x, subject, select=c("arbitrary", "all"), ignore.strand=FALSE)
+\S4method{nearest}{GenomicRanges,missing}(x, subject, select=c("arbitrary", "all"), ignore.strand=FALSE)
 
 \S4method{distanceToNearest}{GenomicRanges,GenomicRanges}(x, subject, ignore.strand=FALSE, ...)
 \S4method{distanceToNearest}{GenomicRanges,missing}(x, subject, ignore.strand=FALSE, ...)

man/tile-methods.Rd

@@ -7,7 +7,7 @@
 
 \description{
   \code{\link[IRanges]{tile}} method for
-  \link{GenomicRanges}. Partitions the each range into a set of
+  \link{GenomicRanges}. Partitions each range into a set of
   tiles. Tiles are defined in terms of their number or width.
 }
 
@@ -31,6 +31,15 @@
   }
 }
 
+\details{
+  Splits \code{x} into a \code{GRangesList}, each element of which corresponds
+  to a tile, or partition, of \code{x}. Specify the tile geometry with either
+  \code{n} or \code{width} (not both). Passing \code{n} creates \code{n} tiles
+  of approximately equal width, truncated by sequence end, while passing
+  \code{width} tiles the region with ranges of the given width, again truncated
+  by sequence end.
+}
+
 \value{
   A \code{GRangesList} object, each element of which corresponds to a tile.
 }