deepblue_liftover: Lift over region results between Genome Assemblies used in...

In DeepBlueR: DeepBlueR

Description

This is a wrapper function for the liftOver function found in the rtracklayer package. For common genome assemblies available in DeepBlue, this function automatically downloads the necessary chain file and calls liftOver.

Usage

deepblue_liftover(regions, source = "hg19", target = "hg38",
  collapse = TRUE)

Arguments

regions	The GRanges object to lift over to another assembly
source	The source assembly version, e.g. hg38. If NULL, we try to read the genome version from the GRanges object.
target	The target assembly version, e.g. hg19. Required.
collapse	Whether to return a single GRanges object or a list of GRanges (one per region in the input). The latter is the default behavior of liftOver since multiple assignments are possible.

Value

A GRanges object using the target chromosome positions

Examples

data_id = deepblue_select_experiments(
experiment_name="E002-H3K9ac.narrowPeak.bed", chromosome="chr1")
request_id = deepblue_get_regions(query_id =data_id,
                                 output_format = "CHROMOSOME,START,END")
request_data = deepblue_download_request_data(request_id)
deepblue_liftover(request_data, source = "hg38", target = "hg19")

DeepBlueR documentation built on Nov. 8, 2020, 6:25 p.m.