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Convert a microhaplotype calls table into PMO microhaplotype structures

pmo_mhap_table_to_pmo.Rd

Builds the representative_microhaplotypes and detected_microhaplotypes components from a long table of microhaplotype calls. The result is a name-based intermediate (see file notes) suitable for pmo_merge_to_pmo().

Usage

pmo_mhap_table_to_pmo(
  microhaplotype_table,
  bioinformatics_run_name = NULL,
  library_sample_name_col = "library_sample_name",
  target_name_col = "target_name",
  seq_col = "seq",
  reads_col = "reads",
  genome_id = 1,
  umis_col = NULL,
  chrom_col = NULL,
  start_col = NULL,
  end_col = NULL,
  ref_seq_col = NULL,
  strand_col = NULL,
  alt_annotations_col = NULL,
  masking_seq_start_col = NULL,
  masking_seq_segment_size_col = NULL,
  masking_replacement_size_col = NULL,
  masking_delim = ",",
  microhaplotype_name_col = NULL,
  pseudocigar_col = NULL,
  pseudocigar_chrom_col = NULL,
  pseudocigar_start_col = NULL,
  pseudocigar_end_col = NULL,
  pseudocigar_ref_seq_col = NULL,
  pseudocigar_strand_col = NULL,
  pseudocigar_genome_id = NULL,
  pseudocigar_generation_description_col = NULL,
  quality_col = NULL,
  additional_representative_mhap_cols = NULL,
  additional_mhap_detected_cols = NULL
)

Arguments

microhaplotype_table

A data.frame of microhaplotype calls.

bioinformatics_run_name

Either a column name in the table (one detected set is built per unique value) or a single run name, or NULL.

library_sample_name_col, target_name_col, seq_col, reads_col

Column names for the required fields.

genome_id

1-based genome id for mhap locations (default 1).

umis_col, chrom_col, start_col, end_col, ref_seq_col, strand_col

Optional column names.

alt_annotations_col, microhaplotype_name_col, pseudocigar_col, quality_col

Optional column names.

masking_seq_start_col, masking_seq_segment_size_col, masking_replacement_size_col

Optional masking column names (all three required together).

masking_delim

Delimiter for masking list values.

pseudocigar_chrom_col, pseudocigar_start_col, pseudocigar_end_col, pseudocigar_ref_seq_col, pseudocigar_strand_col, pseudocigar_genome_id, pseudocigar_generation_description_col

Columns/value used to build the Pseudocigar object's ref_loc (GenomicLocation) when pseudocigar_col is set. The chromosome defaults to chrom_col and the genome id to genome_id; pseudocigar_start_col and pseudocigar_end_col are required (an error is raised if pseudocigar_col is set without a constructable ref_loc).

additional_representative_mhap_cols, additional_mhap_detected_cols

Optional extra columns to carry through.

Value

A list with representative_microhaplotypes and a list of detected_microhaplotypes.

Examples

calls <- data.frame(
  library_sample_name = c("S1", "S1", "S2"),
  target_name = c("t1", "t2", "t1"),
  seq = c("ACGT", "TTTT", "ACGA"),
  reads = c(120, 80, 95)
)
mhaps <- pmo_mhap_table_to_pmo(calls)
length(mhaps$representative_microhaplotypes$targets)
#> [1] 2