sgedges-methods: Extract the edges (and nodes) of a splicing graph

In Bioconductor/SplicingGraphs: Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them

Extract the edges (and nodes) of a splicing graph

Description

sgedges (resp. sgnodes) extracts the edges (resp. the nodes) of the splicing graph of a given gene from a SplicingGraphs object.

Usage

sgedges(x, txweight=NULL, keep.dup.edges=FALSE)
sgnodes(x)
outdeg(x)
indeg(x)

Arguments

x	A SplicingGraphs object of length 1.
txweight	TODO
keep.dup.edges	If FALSE (the default), then edges with the same global edge id are merged into a single row. Use keep.dup.edges=TRUE if this merging should not be performed.

Details

TODO

Value

TODO

Author(s)

H. Pagès

See Also

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.

Examples

## ---------------------------------------------------------------------
## 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))
}

Bioconductor/SplicingGraphs documentation built on Nov. 3, 2024, 8:11 a.m.