Mark animals as genotyped on a SNP chip

Records which individuals have been genotyped on a named SNP chip by writing or updating a BOOLEAN column has_<chip_name> in ind_meta. Pipe a tidybreed_table (from get_table() and optionally dplyr::filter()) as the first argument to restrict which animals are marked.

The operation is additive: animals already marked TRUE remain TRUE. Only new animals are flipped. This mirrors real life — once an animal is genotyped it stays genotyped.

Usage

add_genotypes(tbl, chip_name, col_name = paste0("has_", chip_name))

Arguments

tbl

A tidybreed_table object from get_table() (optionally piped through dplyr::filter()). The table must contain an id_ind column when a filter is applied.

chip_name

Character. Name of an existing SNP chip (must have an is_<chip_name> column in genome_meta, created by define_chip()).

col_name

Character. Name of the BOOLEAN column to write in ind_meta. Default: paste0("has_", chip_name).

Value

The modified tidybreed_pop (invisibly).

Examples

if (FALSE) { # \dontrun{
# Genotype all females in generation 1 on the 50k chip
pop <- pop |>
  get_table("ind_meta") |>
  dplyr::filter(sex == "F", gen == 1L) |>
  add_genotypes("50k")

# Also genotype all generation 2 animals (additive — gen 1 females stay TRUE)
pop <- pop |>
  get_table("ind_meta") |>
  dplyr::filter(gen == 2L) |>
  add_genotypes("50k")
} # }