cross: Cross two individuals

In kbroman/simcross: Simulate Experimental Crosses

Cross two individuals

Description

Simulate the cross of two individuals to create a single progeny

Usage

cross(
  mom,
  dad,
  m = 10,
  p = 0,
  xchr = FALSE,
  male = FALSE,
  obligate_chiasma = FALSE,
  Lstar = NULL
)

Arguments

mom	An individual object, as produced by create_parent() or this function.
dad	An individual object, as produced by create_parent() or this function.
m	interference parameter for chi-square model
p	proportion of crossovers coming from no-interference process
xchr	If TRUE, simulate X chromosome
male	If TRUE, simulate a male (matters only if xchr=TRUE)
obligate_chiasma	If TRUE, require an obligate chiasma on the 4-strand bundle at meiosis.
Lstar	Adjusted chromosome length, if obligate_chiasma=TRUE. Calculated if not provided.

Details

Simulations are under the Stahl model with the interference parameter being an integer. This is an extension of the chi-square model, but with chiasmata being the superposition of two processes, one following the chi-square model and the other exhibiting no interference.

Value

A list with two components, for the individual's two chromosomes. Each is a list with alleles in chromosome intervals (as integers) and locations of the right endpoints of those intervals.

See Also

create_parent(), sim_meiosis(), sim_crossovers(), calc_Lstar()

Examples

mom <- create_parent(100, 1:2)
dad <- create_parent(100, 1:2)
child <- cross(mom, dad)

kbroman/simcross documentation built on Jan. 13, 2024, 10:31 p.m.