twoMarkerDistribution: Genotype probability distribution
In paramlink: Parametric Linkage and Other Pedigree Analysis in R

twoMarkerDistribution

R Documentation

Genotype probability distribution

Description

Computes the joint genotype distribution of two markers for a specified pedigree member, conditional on existing genotypes and pedigree information.

Usage

twoMarkerDistribution(
  x,
  id,
  partialmarker1,
  partialmarker2,
  theta,
  loop_breakers = NULL,
  eliminate = 99,
  verbose = TRUE
)

Arguments

`x`	A `linkdat` object.
`id`	The individual in question.
`partialmarker1, partialmarker2`	Either a single integer indicating the number of one of `x`'s existing markers, or a `marker` object.
`theta`	A single numeric in the interval [0, 0.5] - the recombination fraction between the two markers.
`loop_breakers`	A numeric containing IDs of individuals to be used as loop breakers. Relevant only if the pedigree has loops. See `breakLoops`.
`eliminate`	A non-negative integer, indicating the number of iterations in the internal genotype-compatibility algorithm. Positive values can save time if `partialmarker` is non-empty and the number of alleles is large.
`verbose`	A logical.

Value

A named matrix giving the joint genotype distribution.

Examples

x = nuclearPed(2)
emptySNP = marker(x, alleles=c('a','b'))
SNP1 = marker(x, 1, c(1,1), 2, c(1,0), alleles=1:2, afreq=c(0.1, 0.9))
twoMarkerDistribution(x, id=2, emptySNP, SNP1, theta=0)
twoMarkerDistribution(x, id=2, emptySNP, SNP1, theta=0.5)
twoMarkerDistribution(x, id=3, emptySNP, SNP1, theta=0.5)

# X-linked example
SNPX_1 = marker(x, 2, c('a','b'), 3, 'b', alleles=c('a','b'), chrom=23)
SNPX_2 = marker(x, 2, c('a','b'), 3, 'b', alleles=c('a','b'), chrom=23)
r1 = twoMarkerDistribution(x, id=4, SNPX_1, SNPX_2, theta=0)
r2 = twoMarkerDistribution(x, id=4, SNPX_1, SNPX_2, theta=0.5)
stopifnot(all(r1==c(.5,0,0,.5)), all(r2==c(.25,.25,.25,.25)))

paramlink documentation built on April 15, 2022, 9:06 a.m.