# oneMarkerDistribution: Genotype distribution for a single marker In pedprobr: Probability Computations on Pedigrees

 oneMarkerDistribution R Documentation

## 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
)
```

### 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` 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

`twoMarkerDistribution()`

### 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) = "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)

```

pedprobr documentation built on June 7, 2022, 9:06 a.m.