rtracklayer: asBED – R documentation

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asBED

Coerce to BED structure

Coerce the structure of an object to one following BED-like conventions, i.e., with columns for blocks and thick regions.

asBED(x, ...)
## S4 method for signature 'GRangesList'
asBED(x)
## S4 method for signature 'GAlignments'
asBED(x)

`x`	Generally, a tabular object to structure as BED
`...`	Arguments to pass to methods

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.

A GRanges, with the columns name, blockStarts and blockSizes added.

Michael Lawrence

## Not run: 
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
exons <- exonsBy(TxDb_Hsapiens_UCSC_hg19_knownGene)
mcols(asBED(exons))

## End(Not run)

R interface to genome annotation files and the UCSC genome browser

v1.50.0

Artistic-2.0 + file LICENSE

Authors

Michael Lawrence, Vince Carey, Robert Gentleman

Initial release