add "A quick introduction to GRanges and GRangesList objects" (slides)

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@99039 bc3139a8-67e5-0310-9ffc-ced21a209358
RamsinghLab · Feb 4, 2015 · b431ff3 · b431ff3
1 parent ed901e7
commit b431ff3
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -7,7 +7,7 @@ Description: The ability to efficiently represent and manipulate genomic
 	intervals. Specialized containers for representing and manipulating
 	short alignments against a reference genome are defined in the
 	GenomicAlignments package.
-Version: 1.19.35
+Version: 1.19.36
 Author: P. Aboyoun, H. Pages and M. Lawrence
 Maintainer: Bioconductor Package Maintainer <[email protected]>
 biocViews: Genetics, Infrastructure, Sequencing, Annotation, Coverage,

diff --git a/R/findOverlaps-methods.R b/R/findOverlaps-methods.R
@@ -192,8 +192,8 @@ setMethod("findOverlaps", c("GenomicRanges", "GenomicRanges"),
 {
     q_ranges <- ranges(query)[queryHits(hits)]
     s_ranges <- ranges(subject)[subjectHits(hits)]
-    1L + pmin(end(q_ranges), end(s_ranges)) -
-         pmax(start(q_ranges), start(s_ranges))
+    1L + pmin.int(end(q_ranges), end(s_ranges)) -
+         pmax.int(start(q_ranges), start(s_ranges))
 }
 
 .aggregated_sum <- function(x, f1, f2)

diff --git a/R/tileGenome.R b/R/tileGenome.R
@@ -31,7 +31,7 @@
 .superimpose_breakpoints <- function(old_breakpoints, new_breakpoints)
 {
     ## Set names on 'new_breakpoints'.
-    new_breakpoints <- pmin(new_breakpoints, tail(old_breakpoints, 1))
+    new_breakpoints <- pmin.int(new_breakpoints, tail(old_breakpoints, 1))
     new2old <- 1L + findInterval(new_breakpoints - 1L, old_breakpoints)
     names(new_breakpoints) <- names(old_breakpoints)[new2old]