sgedges-methods {SplicingGraphs} | R Documentation |
sgedges
(resp. sgnodes
) extracts the edges (resp. the nodes)
of the splicing graph of a given gene from a SplicingGraphs object.
sgedges(x, txweight=NULL, keep.dup.edges=FALSE) sgnodes(x) outdeg(x) indeg(x)
x |
A SplicingGraphs object of length 1. |
txweight |
TODO |
keep.dup.edges |
If |
TODO
TODO
H. Pagès
This man page is part of the SplicingGraphs package.
Please see ?`SplicingGraphs-package`
for an overview of the
package and for an index of its man pages.
## --------------------------------------------------------------------- ## 1. Make SplicingGraphs object 'sg' from toy gene model (see ## '?SplicingGraphs') ## --------------------------------------------------------------------- example(SplicingGraphs) # create SplicingGraphs object 'sg' sg ## 'sg' has 1 element per gene and 'names(sg)' gives the gene ids. names(sg) ## --------------------------------------------------------------------- ## 2. Basic usage ## --------------------------------------------------------------------- sgedges(sg["geneD"]) sgnodes(sg["geneD"]) outdeg(sg["geneD"]) indeg(sg["geneD"]) ## --------------------------------------------------------------------- ## 3. Sanity checks ## --------------------------------------------------------------------- check_way1_vs_way2 <- function(res1, res2) { edges1 <- res1[res1$ex_or_in != "", ] # remove artificial edges edges2 <- mcols(unlist(res2, use.names=FALSE)) stopifnot(identical(edges1, edges2)) } for (i in seq_along(sg)) { sgi <- sg[i] ## After removal of the artificial edges, the edges returned ## by 'sgedges()' should be the same as those returned ## by 'sgedgesByGene()' on a SplicingGraphs object of length 1. check_way1_vs_way2( sgedges(sgi), sgedgesByGene(sgi)) ## After removal of the artificial edges, the edges returned ## by 'sgedges( , keep.dup.edges=TRUE)' should be the same as ## those returned by 'sgedgesByGene( , keep.dup.edges=TRUE)' or by ## 'sgedgesByTranscript()' on a SplicingGraphs object of length 1. res1 <- DataFrame(sgedges(sgi, keep.dup.edges=TRUE)) check_way1_vs_way2( res1, sgedgesByGene(sgi, keep.dup.edges=TRUE)) check_way1_vs_way2( res1, sgedgesByTranscript(sgi)) }