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
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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) |