Marker simulation
Simulates marker genotypes conditional on the pedigree structure, affection statuses and disease model.
markerSim(x, N = 1, available = NULL, alleles = NULL, afreq = NULL, partialmarker = NULL, loop_breakers = NULL, eliminate = 0, seed = NULL, verbose = TRUE)
x |
a |
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 |
afreq |
a vector of length 2 containing the population frequencies for
the marker alleles. Must be NULL if |
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 |
loop_breakers |
a numeric containing IDs of individuals to be used as
loop breakers. Relevant only if the pedigree has loops, and only if
|
eliminate |
A non-negative integer, indicating the number of iterations
in the internal genotype-compatibility algorithm. Positive values can save
time if |
seed |
NULL, or a numeric seed for the random number generator. |
verbose |
a logical. |
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.
a linkdat object equal to x except its
markerdata entry, which consists of the N simulated markers.
Magnus Dehli Vigeland
G. M. Lathrop, J.-M. Lalouel, C. Julier, and J. Ott, Strategies for Multilocus Analysis in Humans, PNAS 81(1984), pp. 3443-3446.
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)
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