\name{rsgedgesByGene-methods}
 
 \alias{rsgedgesByGene-methods}
 
 \alias{uninformativeSSids}
 \alias{uninformativeSSids,ANY-method}
 \alias{uninformativeSSids,DataFrame-method}
 
 \alias{rsgedgesByTranscript}
 \alias{rsgedgesByTranscript,SplicingGraphs-method}
 
 \alias{rsgedgesByGene}
 \alias{rsgedgesByGene,SplicingGraphs-method}
 
 \alias{rsgedges}
 \alias{sgedges2}
 
 \alias{rsgraph}
 \alias{sgraph2}
 
 
 \title{
   Extract the reduced edges and their ranges from a SplicingGraphs object
 }
 
 \description{
   \code{rsgedgesByGene} and \code{rsgedgesByTranscript} are analog to
   \code{\link{sgedgesByGene}} and \code{\link{sgedgesByTranscript}},
   but operate on the \emph{reduced} splicing graphs, that is, the
   graphs in \link{SplicingGraphs} object \code{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.
 
   \code{rsgedges} extracts the edges of the reduced splicing graph of
   a given gene from a \link{SplicingGraphs} object.
 
   \code{rsgraph} extracts the reduced splicing graph for a given gene
   from a \link{SplicingGraphs} object, and returns it as a plottable
   graph-like object.
 }
 
 \usage{
 rsgedgesByGene(x, with.hits.mcols=FALSE, keep.dup.edges=FALSE)
 
 rsgedgesByTranscript(x, with.hits.mcols=FALSE)
 
 rsgedges(x)
 
 rsgraph(x, tx_id.as.edge.label=FALSE, as.igraph=FALSE)
 
 ## Related utility:
 uninformativeSSids(x)
 }
 
 \arguments{
   \item{x}{
     A \link{SplicingGraphs} object. Must be of length 1 for \code{rsgedges},
     \code{rsgraph}, and \code{uninformativeSSids}.
   }
   \item{with.hits.mcols}{

     Whether or not to include the \emph{hits metadata columns} in the
     returned object. See \code{?\link{countReads}} for more information.

   }
   \item{keep.dup.edges}{

     Not supported yet.

   }
   \item{tx_id.as.edge.label}{

     Whether or not to use the transcript ids as edge labels.

   }
   \item{as.igraph}{
     TODO
   }
 }
 
 \details{

   TODO: Explain graph reduction.

 }
 
 \value{

   For \code{rsgedgesByGene}: A \link[GenomicRanges]{GRangesList} object
   named with the gene ids and where the reduced splicing graph edges are
   grouped by gene.
 
   TODO: Explain values returned by the other function.

 }
 
 \author{
   H. Pages
 }
 
 \seealso{

   This man page is part of the \pkg{SplicingGraphs} package.

   Please see \code{?`\link{SplicingGraphs-package}`} for an overview of the
   package and for an index of its man pages.
 }
 
 \examples{
 ## ---------------------------------------------------------------------
 ## 1. Make SplicingGraphs object 'sg' from toy gene model (see
 ##    '?SplicingGraphs')
 ## ---------------------------------------------------------------------
 example(SplicingGraphs)
 sg
 
 ## 'sg' has 1 element per gene and 'names(sg)' gives the gene ids.
 names(sg)
 
 ## ---------------------------------------------------------------------
 ## 2. rsgedgesByGene()
 ## ---------------------------------------------------------------------
 edges_by_gene <- rsgedgesByGene(sg)
 edges_by_gene
 ## 'edges_by_gene' has the length and names of 'sg', that is, the names
 ## on it are the gene ids and are guaranteed to be unique.
 
 ## Extract the reduced edges and their ranges for a given gene:
 edges_by_gene[["geneA"]]
 ## Note that edge with global reduced edge id "geneA:1,2,4,5" is a mixed
 ## edge obtained by combining together edges "geneA:1,2" (exon),
 ## "geneA:2,4" (intron), and "geneA:4,5" (exon), during the graph
 ## reduction.
 

 stopifnot(identical(edges_by_gene["geneB"], rsgedgesByGene(sg["geneB"])))
 

 ## ---------------------------------------------------------------------
 ## 3. sgedgesByTranscript()
 ## ---------------------------------------------------------------------
 #edges_by_tx <- rsgedgesByTranscript(sg)  # not ready yet!
 #edges_by_tx
 
 ## ---------------------------------------------------------------------
 ## 4. rsgedges(), rsgraph(), uninformativeSSids()
 ## ---------------------------------------------------------------------
 plot(sgraph(sg["geneB"]))
 uninformativeSSids(sg["geneB"])
 
 plot(rsgraph(sg["geneB"]))
 rsgedges(sg["geneB"])
 
 ## ---------------------------------------------------------------------
 ## 5. Sanity checks
 ## ---------------------------------------------------------------------
 ## TODO: Do the same kind of sanity checks that are done for sgedges()
 ## vs sgedgesByGene() vs sgedgesByTranscript() (in man page for sgedges).
 }