Skip to contents

Define a chromosome's inheritance or recombination rule

Source: R/define_chromosome.R
define_chromosome.Rd

Sets a non-default rule for one chromosome — sex chromosomes (X/Y, Z/W, X0/Z0) and organelles (mitochondria, plastids). define_genome() seeds every chromosome with the default diploid-autosome rule (one copy from each parent, recombining in both sexes); call define_chromosome() before add_founders() to override that default.

The rule is stored across two explicit long tables, and each call sets exactly one concern:

  • Inheritance (copy count): supply from_parent_1 and from_parent_2 — the number of copies of this chromosome an offspring of offspring_sex inherits from parent_1 (sire) and parent_2 (dam). Writes chr_inheritance.

  • Recombination: supply recombines — whether a parent of parent_sex recombines this chromosome when making gametes. Writes chr_recombination.

Copy counts are absolute (correct at ploidy 2, which this version enforces): an autosome is from_parent_1 = 1, from_parent_2 = 1; a male's X is 0, 1; a male's Y is 1, 0; a female's Y is 0, 0; maternal mitochondria are 0, 1. The two concerns are kept in separate calls because "which sex" means the offspring for copy count but the producing parent for recombination — mixing them in one call would make that ambiguous.

Usage

define_chromosome(
  pop,
  chr_name,
  offspring_sex = NULL,
  parent_sex = NULL,
  line_name = NULL,
  from_parent_1 = NULL,
  from_parent_2 = NULL,
  recombines = NULL,
  overwrite = TRUE
)

Arguments

pop

A tidybreed_pop object.

chr_name

Character scalar. Must already exist as a genome_meta.chr_name value (defined via define_genome()'s chr_names argument).

offspring_sex

NULL (default; the sex-agnostic default row), "M", or "F". The inheritance row key — the offspring sex whose copy counts this call sets. Only valid on an inheritance call.

parent_sex

NULL (default; both parent sexes), "M", or "F". The recombination row key — the producing-parent sex whose recombination this call sets. Only valid on a recombination call.

line_name

NULL (default; all lines) or a line name. Reserved for line-specific rules (crossbreeding); resolves with the same precedence as the sex dimension.

from_parent_1, from_parent_2

Non-negative integers supplied together on an inheritance call. Copies inherited from parent_1 (sire) and parent_2 (dam); their sum must be <= 2 in this diploid release.

recombines

Single logical supplied on a recombination call. TRUE if the chromosome recombines during gamete formation, FALSE for non-recombining chromosomes (Y, W, MT, most organelles). For a genome-wide achiasmatic sex, set recombines_M/recombines_F on define_genome() instead of one call per chromosome.

overwrite

Logical. TRUE (default) upserts the row for this logical key. FALSE errors if the exact (chr_name, sex, line_name) key already exists (note: define_genome() pre-seeds the (chr, NULL, NULL) default row, so overwrite = FALSE on a default-keyed call always collides — it is meant for guarding new sex/line-specific rows).

Value

The tidybreed_pop (invisibly). Assign the result back.

See also

define_genome()

Examples

if (FALSE) { # \dontrun{
pop <- open_pop(pop_name = "test", db_name = ":memory:") |>
  define_genome(n_loci = 1000, n_chr = 3, chr_len_Mb = 100,
                chr_names = c("1", "X", "Y"))

# Mammalian sex chromosomes — inheritance (override only the deviating sexes)
pop <- pop |>
  define_chromosome("X", offspring_sex = "M", from_parent_1 = 0, from_parent_2 = 1) |>
  define_chromosome("Y", offspring_sex = "M", from_parent_1 = 1, from_parent_2 = 0) |>
  define_chromosome("Y", offspring_sex = "F", from_parent_1 = 0, from_parent_2 = 0) |>
  # Y is non-recombining (both parent sexes)
  define_chromosome("Y", recombines = FALSE)

# Avian Z/W — females (ZW) are the heterogametic sex, males are ZZ
pop_zw <- open_pop(pop_name = "chicken", db_name = ":memory:") |>
  define_genome(n_loci = 1000, n_chr = 3, chr_len_Mb = 100,
                chr_names = c("1", "Z", "W"))
pop_zw <- pop_zw |>
  define_chromosome("Z", offspring_sex = "F", from_parent_1 = 1, from_parent_2 = 0) |>
  define_chromosome("W", offspring_sex = "F", from_parent_1 = 0, from_parent_2 = 1) |>
  define_chromosome("W", offspring_sex = "M", from_parent_1 = 0, from_parent_2 = 0) |>
  # W is non-recombining (both parent sexes)
  define_chromosome("W", recombines = FALSE)

# Mitochondria — maternal inheritance + non-recombining (separate calls)
pop2 <- open_pop(pop_name = "test2", db_name = ":memory:") |>
  define_genome(n_loci = 1000, n_chr = 2, chr_len_Mb = 100,
                chr_names = c("1", "MT"))
pop2 <- pop2 |>
  define_chromosome("MT", from_parent_1 = 0, from_parent_2 = 1) |>
  define_chromosome("MT", recombines = FALSE)
} # }