markerSim: Marker simulation

In paramlink: Parametric Linkage and Other Pedigree Analysis in R

Marker simulation

Description

Simulates marker genotypes conditional on the pedigree structure, affection statuses and disease model.

Usage

markerSim(
  x,
  N = 1,
  available = NULL,
  alleles = NULL,
  afreq = NULL,
  partialmarker = NULL,
  loop_breakers = NULL,
  eliminate = 0,
  seed = NULL,
  verbose = TRUE
)

Arguments

x	a linkdat object
N	a positive integer: the number of markers to be simulated
available	a vector containing IDs of the available individuals, i.e. those whose genotypes should be simulated. By default, all individuals are included.
alleles	a vector containing the alleles for the marker to be simulation. If a single integer is given, this is interpreted as the number of alleles, and the actual alleles as 1:alleles. Must be NULL if partialmarker is non-NULL.
afreq	a vector of length 2 containing the population frequencies for the marker alleles. Must be NULL if partialmarker is non-NULL.
partialmarker	Either NULL (resulting in unconditional simulation), a marker object (on which the simulation should be conditioned) or the index of an existing marker of x.
loop_breakers	a numeric containing IDs of individuals to be used as loop breakers. Relevant only if the pedigree has loops, and only if partialmarker is non-NULL. 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 is non-NULL and the number of alleles is large.
seed	NULL, or a numeric seed for the random number generator.
verbose	a logical.

Details

This implements (with various time savers) the algorithm used in SLINK of the LINKAGE/FASTLINK suite. If partialmarker is NULL, genotypes are simulated by simple gene dropping, using simpleSim.

Value

a linkdat object equal to x except its markerdata entry, which consists of the N simulated markers.

References

G. M. Lathrop, J.-M. Lalouel, C. Julier, and J. Ott, Strategies for Multilocus Analysis in Humans, PNAS 81(1984), pp. 3443-3446.

See Also

simpleSim, linkage.power

Examples

x = nuclearPed(2)
partial = marker(x, 3, 1, alleles=1:3)
markerSim(x, N=1, alleles=1:3)
markerSim(x, N=1, partialmarker=partial)
markerSim(x, N=1, partialmarker=partial)
markerSim(x, N=1, available=4, partialmarker=partial)

paramlink documentation built on April 15, 2022, 9:06 a.m.