Generate a unified input-QC report — hbr_generate_input_qc

Runs the three input-QC checks — sequence-resource QC ([hbr_validate_sequence_resources()]), genotype-reference compatibility ([hbr_validate_genotype_reference()]), and ID overlap ([hbr_validate_individual_ids()], when phenotypes are supplied) — and prints a single consolidated report. Optionally writes a plain- text file and/or a full report set (TXT + three CSV tables) to `out_dir`. Only the TXT and CSV files are written: the HTML duplicate was removed.

Usage

hbr_generate_input_qc_report(
  reference,
  genotype,
  phenotype_data = NULL,
  pheno_id_col = "ID",
  out_file = NULL,
  out_dir = NULL,
  ...
)

Arguments

reference: A `hbr_reference` object.
genotype: A `hbr_genotype` object.
phenotype_data: Optional phenotype table.
pheno_id_col: ID column in `phenotype_data`.
out_file: Optional single text file path.
out_dir: Optional directory for the full report set.
...: Passed to [hbr_validate_genotype_reference()].

Value

Invisibly, a list with `sequence_qc`, `compatibility`, `id_report`, `overall_status`, and `files`.

Examples

if (interactive()) {
  toy <- system.file("extdata", "toy", package = "HaploBreedR")
  # A complete call needs an hbr_reference and hbr_genotype; see the
  # vignette for the construction used here.
}