Unconditional marker simulation
Unconditional simulation of unlinked markers
simpleSim(x, N, alleles, afreq, available, Xchrom = FALSE, mutmat = NULL, seed = NULL, verbose = T)
x |
a |
N |
a positive integer: the number of markers to be simulated |
alleles |
a vector containing the allele names. If missing, the alleles
are taken to be |
afreq |
a vector of length 2 containing the population frequencies for the alleles. If missing, the alleles are assumed equifrequent. |
available |
a vector containing IDs of the available individuals, i.e. those whose genotypes should be simulated. |
Xchrom |
a logical: X linked markers or not? |
mutmat |
a mutation matrix, or a list of two such matrices named 'female' and 'male'. The matrix/matrices must be square, with the allele labels as dimnames, and each row must sum to 1 (after rounding to 3 decimals). |
seed |
NULL, or a numeric seed for the random number generator. |
verbose |
a logical. |
This simulation is done by distributing alleles randomly to all founders,
followed by unconditional gene dropping down throughout the pedigree (i.e.
for each non-founder a random allele is selected from each of the parents).
Finally the genotypes of any individuals not included in available
are removed.
a linkdat object equal to x in all respects except its
markerdata entry, which consists of the N simulated markers.
Magnus Dehli Vigeland
x = nuclearPed(1) simpleSim(x, N=3, afreq=c(0.5, 0.5)) y = addOffspring(cousinPed(1), father=7, mother=8, noffs=1) simpleSim(y, N=3, alleles=LETTERS[1:10])
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