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,
  loopBreakers = NULL,
  eliminate = 0,
  grid.subset = NULL,
  verbose = TRUE
)

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.

Arguments

x: A ped object or a list of such.
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. If x has multiple components, only the latter is allowed.
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 breakLoops().
eliminate: Deprecated, not used.
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.

Author

Magnus Dehli Vigeland

Examples

Run this code


# 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) = "1/-"
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", afreq = c("1" = 0.5, "2" = 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) |>
  addMarker("9" = "a/a", afreq = c(a = 0.01, b = 0.99))

oneMarkerDistribution(y, ids = 8, partialmarker = 1)