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Extract genotype data for individuals, by chip and/or causal loci

Source: R/extract_genotypes.R
extract_genotypes.Rd

Returns a tibble of genotypes (0/1/2 encoding) for a set of individuals, restricted to loci selected by a chip definition, a filtered genome_effect_loci view, or both. Pipe a tidybreed_table (from get_table() and optionally dplyr::filter()) as the first argument to restrict which individuals are included.

At least one of chip_name or effects_tbl must be provided. When both are given the locus sets are unioned (deduplicated, ordered by locus_id).

Chip path — the returned individual set is the intersection of:

  • Animals with has_<chip_name> == TRUE in ind_meta

  • Animals matching any pending filter() predicates on tbl

  • Loci with is_<chip_name> == TRUE in genome_meta

Causal-locus path (effects_tbl) — the returned individual set is:

  • Animals matching any pending filter() predicates on tbl (or all individuals in ind_haplotype when no filter is applied)

  • Loci whose locus_id appears in the collected effects_tbl

Usage

extract_genotypes(
  tbl,
  chip_name = NULL,
  effects_tbl = NULL,
  loci_tbl = NULL,
  col_name = NULL
)

Arguments

tbl

A tidybreed_table from get_table(), optionally piped through dplyr::filter(). Any table with an id_ind column is accepted; the individuals acted on are the distinct id_ind values present in the (filtered) table. An unfiltered ind_meta selects every individual; an unfiltered ind_ebv, ind_index, ind_genotype, ... selects only the individuals that have rows there. A table without id_ind is an error.

chip_name

Character or NULL. Name of a chip previously defined via define_chip() and applied to animals via add_genotypes(). When NULL the chip path is skipped.

effects_tbl

A tidybreed_table from get_table(pop, "genome_effect_loci") (optionally filtered), or NULL. One row per (term x locus), so use dplyr::filter() to restrict by trait_name, effect_owner, contrast_name, genome_value, or locus_name. Effects are stored as terms over one or more loci, and a multi-locus term contributes every one of its loci. When NULL the causal-locus path is skipped.

loci_tbl

A tidybreed_table from get_table(pop, "genome_meta") (optionally filtered), or NULL. A general locus filter independent of chips and causal-locus sets — e.g. filter(!chr_name %in% c("X", "Y", "MT")) to restrict to autosomes. The collected table's locus_name values become the locus set. Unioned with chip_name/effects_tbl when combined.

col_name

Character. Name of the BOOLEAN column in ind_meta that records chip genotyping status. Default: paste0("has_", chip_name). Ignored when chip_name is NULL.

Value

A tibble with one row per individual and one column per selected locus (id_ind + locus_N columns). Locus columns use 0/1/2 integer encoding and are ordered by locus_id.

Examples

if (FALSE) { # \dontrun{
# All genotyped animals on the 50k chip (unchanged usage)
geno <- pop |> get_table("ind_meta") |> extract_genotypes("50k")

# Only females genotyped on the HD chip
geno <- pop |>
  get_table("ind_meta") |>
  dplyr::filter(sex == "F") |>
  extract_genotypes("HD")

# Every causal locus for a trait (all individuals)
geno <- pop |>
  get_table("ind_meta") |>
  extract_genotypes(
    effects_tbl = get_table(pop, "genome_effect_loci") |>
      dplyr::filter(trait_name == "ADG")
  )

# Additive QTL with a large coefficient, females only
geno <- pop |>
  get_table("ind_meta") |>
  dplyr::filter(sex == "F") |>
  extract_genotypes(
    effects_tbl = get_table(pop, "genome_effect_loci") |>
      dplyr::filter(trait_name == "ADG", contrast_name == "additive",
                    abs(genome_value) > 0.15)
  )

# Chip loci + causal loci unioned
geno <- pop |>
  get_table("ind_meta") |>
  extract_genotypes(
    chip_name   = "50k",
    effects_tbl = get_table(pop, "genome_effect_loci") |>
      dplyr::filter(trait_name == "ADG")
  )
} # }