Carrier status of the superior haplotype at a gene — hbr_gene

Reads the per-gene `<gene>_individuals.csv` written by [haplobreed_analysis()] and returns, for every individual in the HGSI result, whether they carry the pipeline's superior haplotype at that gene. Used to colour per-individual figures by carrier status.

Usage

hbr_gene_carriers(x, trait, gene, trait_dir = NULL, superior_haplotype = NULL)

Arguments

x: An `hgsi_advanced` object.
trait: Trait label.
gene: Gene ID.
trait_dir: Path to the trait's pipeline output directory. If `NULL`, the helper looks in `x$trait_dirs[[trait]]`.
superior_haplotype: Optional. When `NULL` (default), the helper reads it from `superior_genes_summary.csv` in `trait_dir`.

Value

A list with `carrier` (logical, length `length(x$ids)`), `haplotype` (character, the assigned haplotype per individual), `superior_haplotype` (character), and `gene` and `trait`.

Examples

toy <- system.file("extdata", "hgsi_toy", package = "HaploBreedR")
td  <- file.path(toy, "trait_YLD")
if (nzchar(toy) && dir.exists(td)) {
  x <- structure(
    list(ids = sprintf("L%03d", 1:150),
         traits = "YLD",
         trait_dirs = c(YLD = td)),
    class = "hgsi_advanced")
  res <- try(hbr_gene_carriers(
    x, trait = "YLD", gene = "GENE04", trait_dir = td))
}
#> Error : Could not determine superior_haplotype for gene 'GENE04'. Pass it explicitly.