Register a liftover backend

Adds a named liftover backend so it can be selected by name in liftover_intervals(). A backend is a function that performs coordinate translation for a set of intervals; this pluggable design lets the package default to an R-native engine while allowing external tools (e.g. CrossMap) to be swapped in.

Usage

register_liftover_backend(name, fn)

Arguments

name

Character scalar naming the backend.

fn

A function with signature function(intervals, chain, ...) that returns a list with two tibbles:

• mapped: translated features, including a .feature_id column linking each output row to its input row in intervals.

• unmapped: the input rows (carrying .feature_id) that produced no output.

Value

Invisibly, the backend name.

Details

intervals passed to a backend is guaranteed to have columns seqnames, start, end, an optional strand, and a .feature_id integer key added by liftover_intervals().

See also

liftover_backends(), liftover_intervals(), liftover_rtracklayer(), liftover_crossmap()

Examples

# A backend that maps every interval onto itself, then use it by name.
passthrough <- function(intervals, chain, ...) {
  list(
    mapped = tibble::tibble(
      .feature_id = intervals$.feature_id,
      seqnames = intervals$seqnames,
      start = intervals$start,
      end = intervals$end,
      strand = "*"
    ),
    unmapped = intervals[0, , drop = FALSE]
  )
}
register_liftover_backend("passthrough", passthrough)
"passthrough" %in% liftover_backends()
#> [1] TRUE

ints <- data.frame(seqnames = "chr1", start = 100, end = 200)
liftover_intervals(ints, chain = "none", to = "human", backend = "passthrough")
#> 
#> ── TranslationResult (? -> human, backend: passthrough) 
#> • input: 1
#> ✔ mapped: 1 (100%)
#> ✖ unmapped: 0
#> ! multi: 0