Extract specimens matching metadata groupings

Keeps the specimens (and their libraries/results) that satisfy any of the supplied metadata groups, returning the filtered PMO and a per-group count table. A specimen matches a group when it has every field in that group and the field's value is among the group's listed values.

Usage

pmo_extract_samples_by_meta_groupings(pmo, meta_fields_values)

Arguments

pmo

A PortableMicrohaplotypeObject or parsed PMO list.

meta_fields_values

File path or inline specification (see .parse_meta_groupings()).

Value

A list with pmo (a filtered PMO list) and group_counts (a tibble with a group column, one column per field, and a count column).

Examples

p <- read_pmo(
  system.file("extdata", "example_full_pmo.json.gz", package = "pmotoolsr"))
res <- pmo_extract_samples_by_meta_groupings(p, "collection_country=Mozambique")
res$group_counts
#> # A tibble: 1 × 3
#>   group collection_country count
#>   <chr> <chr>              <int>
#> 1 0     Mozambique             2