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

Description Usage Arguments Value Examples

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

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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

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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")

MPIIComputationalEpigenetics/DeepBlueR documentation built on May 8, 2019, 3:19 p.m.