twoMarkerDistribution: Genotype distribution for two linked markers

In pedprobr: Probability Computations on Pedigrees

Genotype distribution for two linked markers

Description

Computes the joint genotype distribution of two markers for a specified pedigree member, conditional on known genotypes and the recombination rate between the markers.

Usage

twoMarkerDistribution(
  x,
  id,
  marker1 = 1,
  marker2 = 2,
  rho = NULL,
  loopBreakers = NULL,
  lumpSpecial = TRUE,
  partialmarker1 = NULL,
  partialmarker2 = NULL,
  verbose = TRUE
)

Arguments

x	A ped object or a list of such.
id	A single ID label.
marker1, marker2	Either marker objects, or the names (or indices) of markers attached to x.
rho	A single numeric in the interval ⁠[0, 0.5]⁠: the recombination fraction between the two markers.
loopBreakers	(Only relevant if the pedigree has loops). A vector with ID labels of individuals to be used as loop breakers. If NULL (default) loop breakers are selected automatically. See pedtools::breakLoops().
lumpSpecial	A logical, passed on to likelihood2().
partialmarker1, partialmarker2	(Deprecated) Aliases for marker1 and marker2.
verbose	A logical.

Value

A named matrix giving the joint genotype distribution.

See Also

oneMarkerDistribution()

Examples

# A sib-pair with two SNPs. The first child is homozygous 1/1.
x = nuclearPed(children = c("bro1", "bro2")) |>
  addMarker(bro1 = "1/1", alleles = 1:2, afreq = c(0.5, 0.5)) |>
  addMarker(bro1 = "1/1", alleles = 1:2, afreq = c(0.5, 0.5))

plot(x, marker = 1:2)

# Genotype distribution for the brother depends on linkage
twoMarkerDistribution(x, id = "bro2", rho = 0)
twoMarkerDistribution(x, id = "bro2", rho = 0.5)

### Same example on X
y = setChrom(x, marker = 1:2, chrom = "X")

plot(y, marker = 1:2)

twoMarkerDistribution(y, id = "bro2", rho = 0)
twoMarkerDistribution(y, id = "bro2", rho = 0.5)

pedprobr documentation built on June 8, 2025, 10:56 a.m.