Retrieve per-analysis translation results from a cohort

After translate() has translated a Cohort, this returns the per-analysis TranslationResult objects (including the unmapped features and mapping statistics) recorded during translation.

Usage

translation_report(cohort)

Arguments

cohort

A Cohort produced by translate().

Value

A named list with from, to, and results (a named list of TranslationResult objects, one per translated analysis), or NULL if the cohort has not been translated.

See also

translate(), TranslationResult

Examples

# A cohort with one gene-level analysis, translated by an in-memory backend.
manifest <- data.frame(
  subject_id = "S1", species = "rat", assay = "rna", sample_id = "R1"
)
parsed <- validate_manifest(manifest)
cohort <- cohort_new(
  parsed$subject_tbl, parsed$sample_map,
  analyses = list(expr = data.frame(gene = c("Tp53", "Myc")))
)
spec <- analysis_spec_new(
  name = "expr", assay = "rna", level = "subject",
  feature_type = "gene", gene_col = "gene", id_type = "symbol"
)
cohort <- analysis_register(cohort, spec)
to_upper <- function(features, from, to, gene_col, id_type, ...) {
  mapped <- features
  mapped$ortholog <- toupper(mapped[[gene_col]])
  list(mapped = mapped, unmapped = features[0, , drop = FALSE])
}
human <- translate(cohort, to = "human", ortholog_backend = to_upper)
#> ✔ Translated 1 analysis: "expr".

report <- translation_report(human)
report$from
#> [1] "rat"
report$to
#> [1] "human"
translation_stats(report$results$expr)
#> # 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 custom        2        2          0       0           1

# NULL for a cohort that has not been translated
translation_report(cohort)
#> NULL