asBED-GInteractions-method: Coerce to BED structure

Description Usage Arguments Value Examples

Description

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

Usage

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## S4 method for signature 'GInteractions'
asBED(x, keep.mcols = FALSE, score = "score")

Arguments

x

Generally, a tabular object to structure as BED

keep.mcols

logical whether to keep non-BED12 columns in final output (may cause problems with some parsers).

score

character, which field to export as "score" in BED12. Defaults to "auto" which will choose score, then counts, if present, or fill column with zeros.

...

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)'.

Value

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

Examples

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Bioconductor-mirror/GenomicInteractions documentation built on June 23, 2017, 6:23 p.m.