# markerSimParametric: Simulate marker data given IBD coefficients In forrel: Forensic Pedigree Analysis and Relatedness Inference

 markerSimParametric R Documentation

## Simulate marker data given IBD coefficients

### Description

This function simulates genotypes for two individuals given their IBD distribution, for N identical markers.

### Usage

``````markerSimParametric(
kappa = NULL,
delta = NULL,
states = NULL,
N = 1,
alleles = NULL,
afreq = NULL,
seed = NULL,
returnValue = c("singletons", "alleles", "genotypes", "internal")
)
``````

### Arguments

 `kappa` A probability vector of length 3, giving a set of realised kappa coefficients (between two noninbred individuals). `delta` A probability vector of length 9, giving a set of condensed identity coefficients (Jacquard coefficients). `states` An integer vector of length `N`, with entries in 1-9. Each entry gives the identity state of the corresponding marker. (See details.) `N` A positive integer: the number of independent markers to be simulated. `alleles` A vector with allele labels. If NULL, the following are tried in order: `names(afreq)` ‘seq_along(afreq)’ `1:2` (fallback if both `alleles` and `afreq` are NULL) `afreq` A numeric vector with allele frequencies, possibly named with allele labels. `seed` An integer seed for the random number generator (optional). `returnValue` Either "singleton" (default) or "alleles". (see Value).

### Details

Exactly one of `kappa`, `delta` and `states` must be given; the other two should remain NULL.

If `states` is given, it explicitly determines the condensed identity state at each marker. The states are described by integers 1-9, using the tradition order introduced by Jacquard.

If `kappa` is given, the states are generated by the command `states = sample(9:7, size = N, replace = TRUE, prob = kappa)`. (Note that identity states 9, 8, 7 correspond to IBD status 0, 1, 2, respectively.)

If `delta` is given, the states are generated by the command `states = sample(1:9, size = N, replace = TRUE, prob = delta)`.

### Value

The output depends on the value of the `returnValue` parameter:

• "singletons": a list of two singletons with the simulated marker data attached.

• "alleles": a list of four vectors of length `N`, named `a`, `b`, `c` and `d`. These contain the simulated alleles, where a/b and c/d are the genotypes of the to individuals.

• "genotypes": a list of two vectors of length `N`, containing the simulated genotypes. Identical to `paste(a, b, sep = "/")` and `paste(c, d, sep = "/")`, where `a`, `b`, `c`, `d` are the vectors returned when `returnValue == "alleles"`.

• "internal": similar to "alleles", but using the index integer of each allele. (This option is mostly for internal use.)

### Examples

``````# MZ twins
markerSimParametric(kappa = c(0,0,1), N = 5, alleles = 1:10)

# Equal distribution of states 1 and 2
markerSimParametric(delta = c(.5,.5,0,0,0,0,0,0,0), N = 5, alleles = 1:10)

# Force a specific sequence of states
markerSimParametric(states = c(1,2,7,8,9), N = 5, alleles = 1:10)

``````

forrel documentation built on Nov. 19, 2023, 5:14 p.m.