# twoMarkerDistribution: Genotype distribution for two linked markers In pedprobr: Probability Computations on Pedigrees

 twoMarkerDistribution R Documentation

## 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,
loopBreakers = NULL,
eliminate = 99,
verbose = TRUE
)
```

### Arguments

 `x` A `ped` object or a list of such. `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. `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 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

`oneMarkerDistribution()`

### 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 = "1/1", afreq = c("1" = 0.5, "2" = 0.5))

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

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