pedprobr: twoMarkerDistribution – R documentation

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twoMarkerDistribution

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,
  partialmarker1,
  partialmarker2,
  rho,
  loop_breakers = NULL,
  eliminate = 99,
  verbose = TRUE
)

Arguments

`x`	A `ped` object.
`id`	A single ID label.
`partialmarker1, partialmarker2`	Either a `marker` object, or the name (or index) of a marker attached to `x`.
`rho`	A single numeric in the interval `[0, 0.5]`: the recombination fraction between the two markers.
`loop_breakers`	(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 `breakLoops()`.
`eliminate`	A non-negative integer, indicating the number of iterations in the internal algorithm for reducing the genotype space. Positive values can save time if `partialmarker1` and/or `partialmarker2` have many alleles.
`verbose`	A logical.

Value

A named matrix giving the joint genotype distribution.

Author(s)

Magnus Dehli Vigeland

Examples

# A sib-pair pedigree
x = nuclearPed(children = c("bro1", "bro2"))

# Two SNP markers; first brother homozygous for the `1` allele
SNP1 = SNP2 = marker(x, bro1 = c(1,1), alleles = 1:2)

plot(x, marker = list(SNP1, SNP2))

# Genotype distribution for the brother: Depends on rho
twoMarkerDistribution(x, id = "bro2", SNP1, SNP2, rho = 0)
twoMarkerDistribution(x, id = "bro2", SNP1, SNP2, rho = 0.5)

# X-linked
chrom(SNP1) = chrom(SNP2) = "X"

plot(x, marker = list(SNP1, SNP2))

twoMarkerDistribution(x, id = "bro2", SNP1, SNP2, rho = 0)
twoMarkerDistribution(x, id = "bro2", SNP1, SNP2, rho = 0.5)

pedprobr

Probability Computations on Pedigrees

v0.5.0

GPL-3

Authors

Magnus Dehli Vigeland [aut, cre] (<https://orcid.org/0000-0002-9134-4962>)

Initial release