git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@119306 bc3139a8-67e5-0310-9ffc-ced21a209358
Herve Pages authored on 12/07/2016 09:05:23
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@76137 bc3139a8-67e5-0310-9ffc-ced21a209358
Herve Pages authored on 30/04/2013 01:20:58
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@@ -90,7 +90,7 @@ uninformativeSSids(x) |
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} |
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\seealso{
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- This man page is part of the SplicingGraphs package. |
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+ This man page is part of the \pkg{SplicingGraphs} package.
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Please see \code{?`\link{SplicingGraphs-package}`} for an overview of the
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package and for an index of its man pages. |
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} |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@76076 bc3139a8-67e5-0310-9ffc-ced21a209358
Herve Pages authored on 26/04/2013 17:59:15
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@@ -59,16 +59,14 @@ uninformativeSSids(x) |
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\code{rsgraph}, and \code{uninformativeSSids}.
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} |
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\item{with.hits.mcols}{
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- TODO |
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+ Whether or not to include the \emph{hits metadata columns} in the
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+ returned object. See \code{?\link{countReads}} for more information.
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} |
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\item{keep.dup.edges}{
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- If \code{FALSE} (the default), then within each group of the returned
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- object, edges with the same \emph{global edge id} are merged into
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- a single element. Use \code{keep.dup.edges=TRUE} if this merging should
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- not be performed. |
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+ Not supported yet. |
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} |
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\item{tx_id.as.edge.label}{
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- TODO |
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+ Whether or not to use the transcript ids as edge labels. |
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} |
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\item{as.igraph}{
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TODO |
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@@ -76,11 +74,15 @@ uninformativeSSids(x) |
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} |
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\details{
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- TODO |
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+ TODO: Explain graph reduction. |
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} |
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\value{
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- TODO |
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+ For \code{rsgedgesByGene}: A \link[GenomicRanges]{GRangesList} object
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+ named with the gene ids and where the reduced splicing graph edges are |
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+ grouped by gene. |
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+ |
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+ TODO: Explain values returned by the other function. |
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} |
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\author{
|
- By default, the output of sgedges() now also includes the "sgedge_id" col,
so it has the same cols as the edge-level metadata cols returned by default
by sgedgesByTranscript() and sgedgesByGene().
- Change the order of the edge-level metadata cols in the GRangesList object
returned by rsgedgesByGene(): the "rsgedge_id" col (global reduced splicing
graph edge id) now is also in 3rd position (instead of 1st), after the
"from" and "to" cols.
- By default, the output of rsgedges() now also includes the "rsgedge_id" col,
so it has the same cols as the edge-level metadata cols returned by default
by rsgedgesByGene().
- The "tx_id" col in the output of all the above functions now is a
CharacterList instead of a broken IntegerList that was holding a factor in
its unlistData slot.
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@75803 bc3139a8-67e5-0310-9ffc-ced21a209358
Herve Pages authored on 19/04/2013 10:13:26
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@@ -119,6 +119,8 @@ edges_by_gene[["geneA"]] |
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## "geneA:2,4" (intron), and "geneA:4,5" (exon), during the graph |
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## reduction. |
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+stopifnot(identical(edges_by_gene["geneB"], rsgedgesByGene(sg["geneB"]))) |
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+ |
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## --------------------------------------------------------------------- |
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## 3. sgedgesByTranscript() |
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## --------------------------------------------------------------------- |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@75782 bc3139a8-67e5-0310-9ffc-ced21a209358
Herve Pages authored on 18/04/2013 19:50:29
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new file mode 100644 |
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+\name{rsgedgesByGene-methods}
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+ |
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+\alias{rsgedgesByGene-methods}
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+ |
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+\alias{uninformativeSSids}
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+\alias{uninformativeSSids,ANY-method}
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+\alias{uninformativeSSids,DataFrame-method}
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+ |
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+\alias{rsgedgesByTranscript}
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+\alias{rsgedgesByTranscript,SplicingGraphs-method}
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+ |
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+\alias{rsgedgesByGene}
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+\alias{rsgedgesByGene,SplicingGraphs-method}
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+ |
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+\alias{rsgedges}
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+\alias{sgedges2}
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+ |
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+\alias{rsgraph}
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+\alias{sgraph2}
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+ |
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+ |
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+\title{
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+ Extract the reduced edges and their ranges from a SplicingGraphs object |
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+} |
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+ |
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+\description{
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+ \code{rsgedgesByGene} and \code{rsgedgesByTranscript} are analog to
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+ \code{\link{sgedgesByGene}} and \code{\link{sgedgesByTranscript}},
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+ but operate on the \emph{reduced} splicing graphs, that is, the
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+ graphs in \link{SplicingGraphs} object \code{x} are reduced before
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+ the edges and their ranges are extracted. The reduced graphs are |
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+ obtained by removing the uninformative nodes from it. See Details |
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+ section below. |
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+ |
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+ \code{rsgedges} extracts the edges of the reduced splicing graph of
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+ a given gene from a \link{SplicingGraphs} object.
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+ |
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+ \code{rsgraph} extracts the reduced splicing graph for a given gene
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+ from a \link{SplicingGraphs} object, and returns it as a plottable
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+ graph-like object. |
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+} |
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+ |
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+\usage{
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+rsgedgesByGene(x, with.hits.mcols=FALSE, keep.dup.edges=FALSE) |
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+ |
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+rsgedgesByTranscript(x, with.hits.mcols=FALSE) |
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+ |
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+rsgedges(x) |
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+ |
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+rsgraph(x, tx_id.as.edge.label=FALSE, as.igraph=FALSE) |
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+ |
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+## Related utility: |
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+uninformativeSSids(x) |
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+} |
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+ |
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+\arguments{
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+ \item{x}{
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+ A \link{SplicingGraphs} object. Must be of length 1 for \code{rsgedges},
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+ \code{rsgraph}, and \code{uninformativeSSids}.
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+ } |
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+ \item{with.hits.mcols}{
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+ TODO |
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+ } |
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+ \item{keep.dup.edges}{
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+ If \code{FALSE} (the default), then within each group of the returned
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+ object, edges with the same \emph{global edge id} are merged into
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+ a single element. Use \code{keep.dup.edges=TRUE} if this merging should
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+ not be performed. |
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+ } |
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+ \item{tx_id.as.edge.label}{
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+ TODO |
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+ } |
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+ \item{as.igraph}{
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+ TODO |
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+ } |
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+} |
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+ |
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+\details{
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+ TODO |
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+} |
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+ |
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+\value{
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+ TODO |
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+} |
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+ |
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+\author{
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+ H. Pages |
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+} |
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+ |
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+\seealso{
|
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+ This man page is part of the SplicingGraphs package. |
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+ Please see \code{?`\link{SplicingGraphs-package}`} for an overview of the
|
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+ package and for an index of its man pages. |
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+} |
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+ |
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+\examples{
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+## --------------------------------------------------------------------- |
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+## 1. Make SplicingGraphs object 'sg' from toy gene model (see |
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+## '?SplicingGraphs') |
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+## --------------------------------------------------------------------- |
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+example(SplicingGraphs) |
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+sg |
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+ |
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+## 'sg' has 1 element per gene and 'names(sg)' gives the gene ids. |
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+names(sg) |
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+ |
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+## --------------------------------------------------------------------- |
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+## 2. rsgedgesByGene() |
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+## --------------------------------------------------------------------- |
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+edges_by_gene <- rsgedgesByGene(sg) |
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+edges_by_gene |
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+## 'edges_by_gene' has the length and names of 'sg', that is, the names |
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+## on it are the gene ids and are guaranteed to be unique. |
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+ |
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+## Extract the reduced edges and their ranges for a given gene: |
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+edges_by_gene[["geneA"]] |
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+## Note that edge with global reduced edge id "geneA:1,2,4,5" is a mixed |
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+## edge obtained by combining together edges "geneA:1,2" (exon), |
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+## "geneA:2,4" (intron), and "geneA:4,5" (exon), during the graph |
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+## reduction. |
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+ |
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+## --------------------------------------------------------------------- |
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+## 3. sgedgesByTranscript() |
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+## --------------------------------------------------------------------- |
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+#edges_by_tx <- rsgedgesByTranscript(sg) # not ready yet! |
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+#edges_by_tx |
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+ |
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+## --------------------------------------------------------------------- |
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+## 4. rsgedges(), rsgraph(), uninformativeSSids() |
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+## --------------------------------------------------------------------- |
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+plot(sgraph(sg["geneB"])) |
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+uninformativeSSids(sg["geneB"]) |
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+ |
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+plot(rsgraph(sg["geneB"])) |
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+rsgedges(sg["geneB"]) |
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+ |
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+## --------------------------------------------------------------------- |
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+## 5. Sanity checks |
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+## --------------------------------------------------------------------- |
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+## TODO: Do the same kind of sanity checks that are done for sgedges() |
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+## vs sgedgesByGene() vs sgedgesByTranscript() (in man page for sgedges). |
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+} |