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. The `blockStarts` and `blockSizes` columns are derived from the ranges in each element. Also, add `name` column from `names(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 1.48.0 Index]