profileSimIBD: Simulate markers conditional on a given IBD pattern

In ibdsim2: Simulation of Chromosomal Regions Shared by Family Members

Simulate markers conditional on a given IBD pattern

Description

This function simulates genotypes for a set of markers conditional on a specific underlying IBD pattern (typically produced with ibdsim()).

Usage

profileSimIBD(
  x,
  ibdpattern,
  ids = NULL,
  markers = NULL,
  seed = NULL,
  verbose = TRUE
)

Arguments

x	A ped object.
ibdpattern	A genomeSim() object, typically created by ibdsim(). (See Examples).
ids	A vector of ID labels. If NULL, extracted from ibdpattern.
markers	A vector with names or indices of markers attached to x.
seed	An integer seed for the random number generator.
verbose	A logical, by default TRUE.

Details

It should be noted that the only random part of this function is the sampling of founder alleles for each marker. Given those, all other genotypes in the pedigree are determined by the underlying IBD pattern.

Value

A copy of x where marker genotypes have been simulated conditional on ibdpattern.

See Also

ibdsim(), forrel::profileSim().

Examples

# Brother-sister pedigree
ped = nuclearPed(2, sex = 1:2)

# Alleles
als = letters[1:10]


### Autosomal simulation

x = ped |> 
  addMarker(alleles = als, chrom = 1, posMb = 20) |> 
  addMarker(alleles = als, chrom = 1, posMb = 50) |> 
  addMarker(alleles = als, chrom = 1, posMb = 70)
  
# Simulate the underlying IBD pattern in the pedigree
sim = ibdsim(x, map = uniformMap(M = 1, chrom = 1), seed = 123)

# Simulate genotypes for the sibs conditional on the given IBD pattern
profileSimIBD(x, sim, ids = 3:4, seed = 123)

# With a different seed
profileSimIBD(x, sim, ids = 3:4, seed = 124)


### X chromosomal simulation

y = ped |> 
  addMarker(alleles = als, chrom = "X", posMb = 1) |> 
  addMarker(alleles = als, chrom = "X", posMb = 50) |> 
  addMarker(alleles = als, chrom = "X", posMb = 100)

simy = ibdsim(y, map = loadMap("decode19", chrom = 23), seed = 11)

profileSimIBD(y, simy, seed = 12)

ibdsim2 documentation built on Aug. 17, 2023, 5:17 p.m.