pedprobr: oneMarkerDistribution – R documentation

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oneMarkerDistribution

Genotype distribution for a single marker

Description

Computes the genotype probability distribution of one or several pedigree members, possibly conditional on known genotypes for the marker.

Usage

oneMarkerDistribution(
  x,
  ids,
  partialmarker,
  loop_breakers = NULL,
  eliminate = 0,
  grid.subset = NULL,
  verbose = TRUE
)

Arguments

`x`	A `ped` object.
`ids`	A numeric with ID labels of one or more pedigree members.
`partialmarker`	Either a `marker` object or the name (or index) of a marker attached to `x`.
`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 genotype-compatibility algorithm. Positive values can save time if `partialmarker` has many alleles.
`grid.subset`	(Optional; not relevant for most users.) A numeric matrix describing a subset of all marker genotype combinations for the `ids` individuals. The matrix should have one column for each of the `ids` individuals, and one row for each combination: The genotypes are described in terms of the matrix `M = allGenotypes(n)`, where `n` is the number of alleles for the marker. If the entry in column `j` is the integer `k`, this means that the genotype of individual `ids[j]` is row `k` of `M`.
`verbose`	A logical.

Value

A named k-dimensional array, where k = length(ids), with the joint genotype distribution for the ids individuals. The probabilities are conditional on the known genotypes and the allele frequencies of partialmarker.

Author(s)

Magnus Dehli Vigeland

Examples

# Trivial example giving Hardy-Weinberg probabilities
s = singleton(id = 1)
m = marker(s, alleles = 1:2) # equifrequent SNP
oneMarkerDistribution(s, ids = 1, partialmarker = m)

# Conditioning on a partial genotype
genotype(m, id = 1) = c(1, NA)
oneMarkerDistribution(s, ids = 1, partialmarker = m)

# Genotype distribution for a child of heterozygous parents
trio = nuclearPed(father = "fa", mother = "mo", child = "ch")
m1 = marker(trio, fa = 1:2, mo = 1:2)
oneMarkerDistribution(trio, ids = "ch", partialmarker = m1)

# Joint distribution of the parents, given that the child is heterozygous
m2 = marker(trio, ch = 1:2, alleles = 1:2, afreq = c(0.5, 0.5))
oneMarkerDistribution(trio, ids = c("fa", "mo"), partialmarker = m2)

# A different example: The genotype distribution of an individual (id = 8)
# whose half cousin (id = 9) is homozygous for a rare allele.
y = halfCousinPed(degree = 1)
snp = marker(y, `9` = "a", alleles = c("a", "b"), afreq = c(0.01, 0.99))
plot(y, snp)
oneMarkerDistribution(y, ids = 8, partialmarker = snp)

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