Extract allele (microhaplotype) counts and frequencies

Tallies, per bioinformatics run and target, how many samples carry each representative microhaplotype, and the within-target frequency. This is the table consumed by downstream tools such as dcifer and moire.

Usage

pmo_extract_allele_counts_freq(
  pmo,
  bioinformatics_run_ids = NULL,
  library_sample_names = NULL,
  target_names = NULL,
  collapse_across_runs = FALSE
)

Arguments

pmo

A PortableMicrohaplotypeObject or parsed PMO list.

bioinformatics_run_ids

Optional integer vector of 1-based run ids to include.

library_sample_names

Optional character vector of library sample names to include.

target_names

Optional character vector of target names to include.

collapse_across_runs

If TRUE, collapse counts/frequencies across runs.

Value

A tibble. If collapse_across_runs = FALSE: columns bioinformatics_run_id, target_name, mhap_id, count, freq, total_haps_per_target. If TRUE: target_name, mhap_id, count, freq, target_total. Note: mhap_id and bioinformatics_run_id are 1-based.

Details

Requires each detected-microhaplotypes set to have a bioinformatics_run_id; an informative error is raised if that optional field is absent.

Examples

p <- read_pmo(
  system.file("extdata", "example_full_pmo.json.gz", package = "pmotoolsr"))
head(pmo_extract_allele_counts_freq(p))
#> # A tibble: 6 × 6
#>   bioinformatics_run_id target_name mhap_id count  freq total_haps_per_target
#>                   <int> <chr>         <int> <int> <dbl>                 <int>
#> 1                     1 t1                1     2   0.5                     4
#> 2                     1 t1                2     2   0.5                     4
#> 3                     1 t10               1     2   1                       2
#> 4                     1 t100              1     1   0.5                     2
#> 5                     1 t100              2     1   0.5                     2
#> 6                     1 t11               1     1   0.5                     2