Browse code

Explicitely sort the hits returned by findOverlaps() (they are not returned fully sorted anymore now that findOverlaps() is based on the NCList algo).

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@98049 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 06/01/2015 07:02:14
Showing 2 changed files

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@@ -1,7 +1,7 @@
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 Package: SplicingGraphs
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 Title: Create, manipulate, visualize splicing graphs, and assign RNA-seq reads
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 	to them
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-Version: 1.7.2
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+Version: 1.7.3
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 Author: D. Bindreither, M. Carlson, M. Morgan, H. Pages
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 License: Artistic-2.0
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 Description: This package allows the user to create, manipulate, and visualize
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@@ -11,9 +11,9 @@ Description: This package allows the user to create, manipulate, and visualize
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         different ways.
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 Maintainer: H. Pages <[email protected]>
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 Depends: BiocGenerics,
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-	 S4Vectors (>= 0.1.0), IRanges (>= 1.99.21), GenomicRanges (>= 1.17.22),
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-	 GenomicFeatures (>= 1.17.13), GenomicAlignments (>= 1.1.22),
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-	 Rgraphviz (>= 2.3.7)
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+	 S4Vectors (>= 0.5.16), IRanges (>= 1.99.21),
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+	 GenomicRanges (>= 1.17.22), GenomicFeatures (>= 1.17.13),
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+	 GenomicAlignments (>= 1.1.22), Rgraphviz (>= 2.3.7)
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 Imports: methods, utils, igraph,
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 	 BiocGenerics,
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 	 IRanges, GenomicRanges, GenomicFeatures, GenomicAlignments,
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@@ -87,7 +87,9 @@ ex_by_tx <- exonsBy(txdb, by="tx", use.names=TRUE)
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 ## should call findOverlaps() with 'ignore.strand=TRUE':
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 ov0 <- findOverlaps(grl, ex_by_tx, ignore.strand=TRUE)
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-## Put the overlaps in a data.frame to make it easier to read:
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+## Sort and put the overlaps in a data.frame to make them easier to
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+## read:
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+ov0 <- sort(ov0)
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 df0 <- data.frame(QNAME=names(grl)[queryHits(ov0)],
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                   tx_id=names(ex_by_tx)[subjectHits(ov0)],
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                   stringsAsFactors=FALSE)