easyLiftOver: easyLiftOver

In caleblareau/easyLift: Convenience package for solving some liftover challenges

Description

Function to get lifted over coordinates using rtracklayer + chain file for a couple of different inputs. Returns all mapped regions as a GRanges/bed file unless "pickOne" is true, in which case the range with the longest genomic positioning will be returned.

Usage

easyLiftOver(from, map = "hg19_hg38", to = NULL, pickOne = FALSE)

Arguments

from	A .bed file or GRanges object containing coordinates to be lifted over.
map	Reference genome mapping logic FROM_TO or alternatively, the filepath associated with a valid .chain file.
to	File to write liftover output to. By default, we just append "over" to the input file name. This parameter is ignored if the user specifies a GRanges object.
pickOne	Choose one region to represent the liftover (the longest) rather than all possible regions (default).

Value

A GRanges if "from" is a GRanges. Otherwise, it will write a file with "over" appeneded with the lifted over coordinates

Examples

from <- paste0(system.file('extdata',package='easyLift'),'/exbed/hg19.quick.bed')
#easyLiftOver(sf, map = "hg19_hg38") # spits out the lifted over bed file
liftedGRanges <- easyLiftOver(from, map = "hg19_hg38")

caleblareau/easyLift documentation built on May 21, 2019, 2:21 p.m.