Power Lifter — power_lifter • biomaesteR

A function to convert genomic regions from one assembly to another.

Usage

power_lifter(
  these_regions = NULL,
  qchrom = NULL,
  qstart = NULL,
  qend = NULL,
  original_assembly = "hg38",
  target_assembly = "grch37"
)

Arguments

these_regions: The region(s) to be queried. Can be a data frame with regions with the following columns; chrom, start, end. Or in a string in the following format chr:start-end.
qchrom: Query chromosome (prefixed or un-prefixed), Required if `these_regions` is not provided.
qstart: Query start position. Required if `these_regions` is not provided.
qend: Query end position. Required if `these_regions` is not provided.
original_assembly: The original assembly of the regions. Default is hg38
target_assembly: The target assembly of the regions. Default is grch37.

Value

A data frame with the regions in the selected target assembly.

Details

This function is a wrapper for the [rtracklayer::liftOver] function. Specify the original assembly and the target assembly, and the function will convert the regions accordingly. Regions can be provided as a data frame with `these_regions`, or as a string with `qchrom`, `qstart`, and `qend`.

Examples

#Example 1 - Convert MYC region from hg38 to grch37
power_lifter(these_regions = "chr8:127735434-127742951")
#>   chrom     start       end width strand
#> 1     8 128747680 128755197  7518      *

#Example 2 - Convert MYC region from grch37 to hg38
power_lifter(these_regions = "18:60790579-60987361", 
             original_assembly = "grch37", 
             target_assembly = "hg38")
#> Discarding unchained sequences: 18
#> [1] chrom  start  end    width  strand
#> <0 rows> (or 0-length row.names)

#Example 3 - Same as Example 1, but use the `qchrom`, `qstart`, and `qend`.
power_lifter(qchrom = "chr8", 
             qstart = 127735434, 
             qend = 127742951)
#>   chrom     start       end width strand
#> 1     8 128747680 128755197  7518      *