Skip to contents

Materialize genotype dosage values into ind_genotype

Source: R/add_dosage.R
add_dosage.Rd

Computes 0/1/2 genotype dosages (sum of alleles across an individual's haplotype strands) from the long ind_haplotype table and writes them to the on-demand ind_genotype cache. ind_genotype is never auto-populated by add_founders() or add_offspring() — call add_dosage() explicitly when you need dosage values for marker-assisted selection, allele-frequency queries, or other downstream analysis.

Pipe a tidybreed_table (from get_table() and optionally dplyr::filter()) as the first argument to select individuals. As with add_tbv(), the distinct id_ind values in the collected table form the candidate set, so a table with multiple rows per individual (e.g. ind_phenotype) does not multiply work.

Usage

add_dosage(tbl, chip_name = NULL, locus_names = NULL, overwrite_dosage = FALSE)

Arguments

tbl

A tidybreed_table from get_table() (optionally filtered). Any table with an id_ind column is accepted.

chip_name

Character or NULL. Name of a chip defined via define_chip() (which writes is_<chip_name> to genome_meta). Loci are restricted to is_<chip_name> = TRUE. Errors if the column is missing.

locus_names

Character vector or NULL. Explicit loci to materialize. Takes precedence over chip_name when both are supplied.

overwrite_dosage

Logical. When TRUE, existing ind_genotype rows for the candidate individuals are deleted before inserting (cache-scope reset). When FALSE (default), rows are upserted via INSERT OR REPLACE — dosage is fully determined by the haplotypes, so re-running is idempotent.

Value

The modified tidybreed_pop (invisibly).

add_dosage() vs. add_genotypes()

These are different operations despite similar names. add_genotypes() marks animals as physically genotyped on a chip by writing a BOOLEAN has_<chip> column to ind_meta; it touches no dosage data. add_dosage() materializes simulated dosage values (ground truth from ind_haplotype) into ind_genotype.

See also

add_genotypes(), extract_genotypes(), define_chip()

Examples

if (FALSE) { # \dontrun{
# Dosage for all generation-5 candidates on the 50K chip
pop <- pop |>
  get_table("ind_meta") |>
  dplyr::filter(gen == 5L) |>
  add_dosage(chip_name = "50K")

# Dosage at specific QTL only
pop <- pop |>
  get_table("ind_meta") |>
  add_dosage(locus_names = c("Locus_1", "Locus_42"))

# Marker-assisted selection: homozygous-favorable at a QTL
ids <- pop |>
  get_table("ind_genotype") |>
  dplyr::filter(locus_name == "Locus_1", dosage_value == 2L) |>
  dplyr::pull(id_ind)
} # }