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The SplicingGraphs class is a container for storing splicing graphs together with the gene model that they are based on.
● Data Source:
BioConductor
● Keywords:
● Alias: GeneModel-class, class:GeneModel
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The SplicingGraphs package allows the user to create, manipulate, and visualize splicing graphs and their bubbles based on a gene model for a given organism. Additionally it allows the user to assign RNA-seq reads to the edges of a set of splicing graphs, and to summarize them in different ways.
● Data Source:
BioConductor
● Keywords: package
● Alias: SplicingGraphs-package
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TODO
● Data Source:
BioConductor
● Keywords:
● Alias: TSPC, TSPCsg
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assignReads assigns reads to the exonic and intronic edges of a SplicingGraphs object.
● Data Source:
BioConductor
● Keywords:
● Alias: assignReads, removeReads
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bubbles computes the bubbles of the splicing graph of a given gene from a SplicingGraphs object.
● Data Source:
BioConductor
● Keywords:
● Alias: bubbles-methods
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countReads counts the reads assigned to a SplicingGraphs object. The counting can be done by splicing graph edge, reduced splicing graph edge, transcript, or gene.
● Data Source:
BioConductor
● Keywords:
● Alias: countReads-methods
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plotTranscripts uses the Gviz package to plot the exon structure of a set of transcripts along genomic coordinates.
● Data Source:
BioConductor
● Keywords:
● Alias: plotTranscripts-methods
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rsgedgesByGene and rsgedgesByTranscript are analog to sgedgesByGene and sgedgesByTranscript, but operate on the reduced splicing graphs, that is, the graphs in SplicingGraphs object x are reduced before the edges and their ranges are extracted. The reduced graphs are obtained by removing the uninformative nodes from it. See Details section below.
● Data Source:
BioConductor
● Keywords:
● Alias: rsgedgesByGene-methods
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sgedges (resp. sgnodes) extracts the edges (resp. the nodes) of the splicing graph of a given gene from a SplicingGraphs object.
● Data Source:
BioConductor
● Keywords:
● Alias: sgedges-methods
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sgedgesByGene and sgedgesByTranscript both extract the edges and their ranges of all the genes from a SplicingGraphs object. They return them in a GRangesList object named with the gene ids, and where the items are grouped by gene (for sgedgesByGene) or by transcript (for sgedgesByTranscript).
● Data Source:
BioConductor
● Keywords:
● Alias: sgedgesByGene-methods
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providing 
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