Description Usage Arguments Details Value Author(s) See Also Examples
Uses the hidden Markov model technology to simulate from the joint distribution Pr(g | O) where g is the underlying genotype vector and O is the observed multipoint marker data, with possible allowance for genotyping errors.
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cross |
An object of class |
n.draws |
Number of simulation replicates to perform. |
step |
Maximum distance (in cM) between positions at which the
simulated genotypes will be drawn, though for |
off.end |
Distance (in cM) past the terminal markers on each chromosome to which the genotype simulations will be carried. |
error.prob |
Assumed genotyping error rate used in the calculation of the penetrance Pr(observed genotype | true genotype). |
map.function |
Indicates whether to use the Haldane, Kosambi, Carter-Falconer, or Morgan map function when converting genetic distances into recombination fractions. |
stepwidth |
Indicates whether the intermediate points should with
fixed or variable step sizes. We recommend using
|
After performing the forward-backward equations, we draw from Pr(g[1] = v | O) and then Pr(g[k+1] = v | O, g[k] = u).
In the case of the 4-way cross, with a sex-specific map, we assume a constant ratio of female:male recombination rates within the inter-marker intervals.
The input cross
object is returned with a component,
draws
, added to each component of cross$geno
.
This is an array of size [n.ind x n.pos x n.draws] where n.pos is
the number of positions at which the simulations were performed and
n.draws is the number of replicates. Attributes "error.prob"
,
"step"
, and "off.end"
are set to the values of the
corresponding arguments, for later reference.
Karl W Broman, kbroman@biostat.wisc.edu
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