asBED {rtracklayer} | R Documentation |
Coerce to BED structure
Description
Coerce the structure of an object to one following BED-like conventions, i.e., with columns for blocks and thick regions.
Usage
asBED(x, ...)
## S4 method for signature 'GRangesList'
asBED(x)
## S4 method for signature 'GAlignments'
asBED(x)
Arguments
x |
Generally, a tabular object to structure as BED |
... |
Arguments to pass to methods |
Details
The exact behavior depends on the class of object
.
GRangesList
This treats
object
as if it were a list of transcripts, i.e., each element contains the exons of a transcript. TheblockStarts
andblockSizes
columns are derived from the ranges in each element. Also, addname
column fromnames(object)
.GAlignments
Converts to GRangesList via
grglist
and procedes accordingly.
Value
A GRanges
, with the columns name
,
blockStarts
and blockSizes
added.
Author(s)
Michael Lawrence
Examples
## Not run:
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
exons <- exonsBy(TxDb_Hsapiens_UCSC_hg19_knownGene)
mcols(asBED(exons))
## End(Not run)
[Package rtracklayer version 1.62.0 Index]