This is the main function of the package, simulating the recombination process in each meioses of a pedigree. The output summarises the IBD segments between all or a subset of individuals.
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A positive integer indicating the number of simulations.
A subset of pedigree members whose IBD sharing should be analysed. If NULL, all members are included.
The genetic map to be used in the simulations: Allowed values are:
Either "chi" or "haldane", indicating the statistical model for recombination (see details). Default: "chi".
A vector of ID labels indicating individuals whose meioses
should be simulated without recombination. (Each child will then receive a
random strand of each chromosome.) The default action is to skip
recombination in founders who are uninformative for IBD sharing in the
An integer to be passed on to
Each simulation starts by unique alleles (labelled 1, 2, ...) being
distributed to the pedigree founders. In each meiosis, homologue chromosomes
are made to recombine according to the value of
model = "haldane": In this model, crossover events are modelled as a
Poisson process along each chromosome.
model = "chi" (default): This uses a renewal process along the
four-strand bundle, with waiting times following a chi square distribution.
Recombination rates along each chromosome are determined by the
parameter. The default value ("decode19") loads a thinned version of the
recombination map of the human genome published by Halldorsson et al (2019).
In many applications, the fine-scale default map is not necessary, and should
be replaced by simpler maps with constant recombination rates. See
loadMap() for ways to produce such maps.
A list of
N objects of class
genomeSim object is essentially a numerical matrix describing the
allele flow through the pedigree in a single simulated. Each row
corresponds to a chromosomal segment. The first 4 columns describe the
segment (chromosome, start, end, length), and are followed by two columns
(paternal allele, maternal allele) for each of the
ids has length 1, a column named "Aut" is added, whose entries are 1
for autozygous segments and 0 otherwise.
ids has length 2, two columns are added:
IBD : The IBD status of each segment (= number of alleles shared
identical by descent). For a given segment, the IBD status is either 0, 1,
2 or NA. If either individual is inbred, they may be autozygous in a
segment, in which case the IBD status is reported as NA. With inbred
Sigma column (see below) is more informative than the
Sigma : The condensed identity ("Jacquard") state of each segment,
given as an integer in the range 1-9. The numbers correspond to the
standard ordering of the condensed states. In particular, for non-inbred
individuals the states 9, 8, 7 correspond to IBD status 0, 1, 2
Halldorsson et al. Characterizing mutagenic effects of recombination through a sequence-level genetic map. Science 363, no. 6425 (2019).
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