git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@113852 bc3139a8-67e5-0310-9ffc-ced21a209358
Herve Pages authored on 22/02/2016 00:08:19
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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: 1.11.2 |
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+Version: 1.11.3 |
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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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@@ -14,7 +14,7 @@ Depends: GenomicFeatures (>= 1.17.13), GenomicAlignments (>= 1.1.22), |
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Rgraphviz (>= 2.3.7) |
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Imports: methods, utils, igraph, BiocGenerics, |
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S4Vectors (>= 0.9.25), IRanges (>= 2.3.21), |
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- GenomeInfoDb, GenomicRanges, GenomicFeatures, Rsamtools, |
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+ GenomeInfoDb, GenomicRanges (>= 1.23.21), GenomicFeatures, Rsamtools, |
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GenomicAlignments, graph, Rgraphviz |
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Suggests: igraph, Gviz, |
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TxDb.Hsapiens.UCSC.hg19.knownGene, RNAseqData.HNRNPC.bam.chr14, |
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@@ -588,7 +588,7 @@ setMethod("SplicingGraphs", "GRangesList",
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check.introns=check.introns) |
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ans_genes <- GeneModel(ans_ex_by_tx) |
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mcols(ans_ex_by_tx) <- NULL |
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- ans_in_by_tx <- psetdiff(range(ans_ex_by_tx), ans_ex_by_tx) |
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+ ans_in_by_tx <- setdiff(range(ans_ex_by_tx), ans_ex_by_tx) |
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common_strand <- commonStrand.GRangesList(ans_in_by_tx) |
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ans_in_by_tx <- revElements(ans_in_by_tx, common_strand == "-") |
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ans_bubbles_cache <- new.env(parent=emptyenv()) |