deepblue_liftover {DeepBlueR} | R Documentation

## Lift over region results between Genome Assemblies used in DeepBlue

### 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")

[Package DeepBlueR version 1.12.0 Index]