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Extract a per-sample allele table

pmo_extract_alleles_per_sample_table.Rd

Builds a long table of library sample, target, and representative microhaplotype sequence, with optional additional metadata columns. This is the table consumed by downstream tools (dcifer, moire, ...).

Usage

pmo_extract_alleles_per_sample_table(
  pmo,
  additional_specimen_info_fields = NULL,
  additional_library_sample_info_fields = NULL,
  additional_microhap_fields = NULL,
  additional_representative_info_fields = NULL,
  default_base_col_names = c("library_sample_name", "target_name", "seq"),
  validate = FALSE
)

Arguments

pmo

A PortableMicrohaplotypeObject or parsed PMO list.

additional_specimen_info_fields, additional_library_sample_info_fields, additional_microhap_fields, additional_representative_info_fields

Optional character vectors of extra fields to include from the respective objects; an error is raised if a requested field exists nowhere.

default_base_col_names

Length-3 character vector naming the sample, target, and sequence columns.

validate

If TRUE, validate the PMO against the schema first.

Value

A tibble.

Examples

pmo <- read_pmo(
  system.file("extdata", "example_pmo.json.gz", package = "pmotoolsr"))
head(pmo_extract_alleles_per_sample_table(pmo))
#> # A tibble: 6 × 4
#>   library_sample_name target_name seq                     bioinformatics_run_n…¹
#>   <chr>               <chr>       <chr>                   <chr>                 
#> 1 SRR30825770         SA_1021483  CAATATAATAACCTAATAAAAT… detected_microhaploty…
#> 2 SRR30825770         SA_11537    AAAGGTAAAGAAGTTTCTGTAA… detected_microhaploty…
#> 3 SRR30825770         SA_11580    TGCGCCGACCATTTATGGTGGT… detected_microhaploty…
#> 4 SRR30825770         SA_1281766  TAGCATTTGTAAATGAAAGTAA… detected_microhaploty…
#> 5 SRR30825770         SA_131432   GATAAGCTGATGCGTTACATTA… detected_microhaploty…
#> 6 SRR30825770         SA_166442   GTTTCATAAAAAAACCACCTTT… detected_microhaploty…
#> # ℹ abbreviated name: ¹​bioinformatics_run_name