Define a SNP chip

Marks the loci in a filtered genome_meta table as members of a SNP chip, creating a BOOLEAN column (default: is_{chip_name}) in genome_meta.

Pipe get_table("genome_meta") — optionally piped through dplyr::filter() — into this function. The unique locus_id values in the collected result determine chip membership. All other loci receive FALSE.

This replaces the old positional selection methods (n/method, locus_tf, locus_ids, locus_names). Selection is now done entirely by the caller using standard dplyr verbs on the genome_meta table, which is order-safe and compatible with dynamic genomes.

Usage

define_chip(tbl, chip_name, col_name = paste0("is_", chip_name))

Arguments

tbl

A tidybreed_table from get_table("genome_meta") (optionally piped through dplyr::filter()). Must contain a locus_id column.

chip_name

Character scalar. Name of the SNP chip; used in messages and to derive the default column name.

col_name

Character scalar. Column name created in genome_meta. Default: paste0("is_", chip_name). Must be a valid SQL identifier.

Value

The modified tidybreed_pop object (invisibly).

See also

define_additive_effects(), add_genotypes(), extract_genotypes()

Examples

if (FALSE) { # \dontrun{
# All loci on chromosomes 1-5
pop <- pop |>
  get_table("genome_meta") |>
  dplyr::filter(chr %in% 1:5) |>
  define_chip("chr1to5")

# Random chip — sample locus names, then filter
selected <- pop |>
  get_table("genome_meta") |>
  dplyr::collect() |>
  dplyr::slice_sample(n = 500) |>
  dplyr::pull(locus_name)

pop <- pop |>
  get_table("genome_meta") |>
  dplyr::filter(locus_name %in% selected) |>
  define_chip("50K")

# Complement of an existing chip
pop <- pop |>
  get_table("genome_meta") |>
  dplyr::filter(is_50K == FALSE) |>
  define_chip("non50K")
} # }