lift_bed: Convert BED intervals between genome builds
In Townsend-Lab-Yale/cancereffectsizeR: Calculate Cancer Effect Size

lift_bed

R Documentation

Convert BED intervals between genome builds

Description

Use this utility to convert BED intervals between genome coordinate systems using liftOver. Only the chr/start/end fields of the input BED are used (strand is ignored). The output GRanges will have no associated seqinfo.

Usage

lift_bed(bed, chain, outfile = NULL)

Arguments

`bed`	Pathname of a BED file, or a GRanges (typically loaded from a BED file with `rtracklayer::import.bed()`).
`chain`	A UCSC-style chain file, or a Chain object (such as from `rtracklayer::import.chain()`).
`outfile`	If not NULL, the returned GRanges will be saved to the specified path using `rtracklayer::export.chain()`.

Details

A warning is given if the lifted intervals are less than 95% of the size of the original intervals. When the BED input represents sequencing target intervals, most of the input intervals will usually lift successfully.