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Merge name-based PMO components into a complete PMO

pmo_merge_to_pmo.Rd

Assembles the outputs of the other builders into a full PMO, replacing every name reference with its 1-based index. If specimen_info/library_sample_info are omitted they are derived from the detected microhaplotypes.

Usage

pmo_merge_to_pmo(
  mhap_info,
  panel_target_info,
  specimen_info = NULL,
  library_sample_info = NULL,
  sequencing_info = NULL,
  bioinfo_method_info = NULL,
  bioinfo_run_info = NULL,
  project_info = NULL,
  read_counts_by_stage_info = NULL
)

Arguments

mhap_info

List with representative_microhaplotypes and detected_microhaplotypes (from pmo_mhap_table_to_pmo()).

panel_target_info

List with panel_info and target_info (and optionally targeted_genomes) from pmo_panel_info_table_to_pmo().

specimen_info, library_sample_info

Optional name-based metadata lists (from pmo_specimen_info_table_to_pmo() / pmo_library_sample_info_table_to_pmo()).

sequencing_info, bioinfo_method_info, bioinfo_run_info, project_info

Optional component lists.

read_counts_by_stage_info

Optional list from pmo_read_count_by_stage_table_to_pmo().

Value

A complete PMO as a raw nested list (1-based ids). Write with write_pmo_raw(), convert with pmo_list_to_r6(), or validate with pmo_validate().

Examples

calls <- data.frame(
  library_sample_name = c("S1", "S2"), target_name = c("t1", "t1"),
  seq = c("ACGT", "ACGA"), reads = c(120, 95))
mhaps <- pmo_mhap_table_to_pmo(calls)
primers <- data.frame(target_name = "t1", fwd_primer = "AAAA",
                      rev_primer = "TTTT")
panel <- pmo_panel_info_table_to_pmo(primers, "demo_panel")
pmo <- pmo_merge_to_pmo(mhap_info = mhaps, panel_target_info = panel)
pmo_validate(pmo)