Result of a cross-species or cross-assembly translation

An S7 class holding the outcome of translating coordinate features or gene-level features from one species or assembly to another. It keeps the successfully translated features, the features that failed to map, and provenance so that translation is never lossy silently.

Usage

TranslationResult(
  mapped = NULL,
  unmapped = NULL,
  from = NA_character_,
  to = NA_character_,
  backend = NA_character_,
  stats = list()
)

Arguments

mapped: A tibble of successfully translated features. Includes a .feature_id column linking each output row back to its input row; one input may yield multiple output rows (multi-mapping).
unmapped: A tibble of input features that produced no output.
from: Character scalar naming the source species/assembly. Optional.
to: Character scalar naming the target species/assembly. Optional.
backend: Character scalar naming the translation backend used. Optional.
stats: Named list of summary counts (n_input, n_mapped, n_unmapped, n_multi).

Value

A TranslationResult object with the given properties.

Details

Construct these via liftover_intervals() or translate() rather than directly. Access the pieces with result@mapped, result@unmapped, and translation_stats().

Examples

# Built by hand here to show the shape; translate() builds them for you.
res <- TranslationResult(
  mapped = tibble::tibble(.feature_id = 1L, gene = "Tp53", ortholog = "TP53"),
  unmapped = tibble::tibble(.feature_id = 2L, gene = "Gm12345"),
  from = "rat",
  to = "human",
  backend = "by_hand",
  stats = list(n_input = 2L, n_mapped = 1L, n_unmapped = 1L, n_multi = 0L)
)
res@unmapped
#> # A tibble: 1 × 2
#>   .feature_id gene   
#>         <int> <chr>  
#> 1           2 Gm12345
translation_stats(res)
#> # A tibble: 1 × 8
#>   from  to    backend n_input n_mapped n_unmapped n_multi prop_mapped
#>   <chr> <chr> <chr>     <int>    <int>      <int>   <int>       <dbl>
#> 1 rat   human by_hand       2        1          1       0         0.5