| sim.geno {qtl} | R Documentation |
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.
sim.geno(cross, n.draws=1, step=0, off.end=0, error.prob=0,
map.function=c("haldane","kosambi","c-f"))
cross |
An object of class cross. See
read.cross for details. |
n.draws |
Number of simulation replicates to perform. |
step |
Maximum number of cM between positions at which the
simulated genotypes will be drawn, though for step = 0,
genotypes are drawn only at the marker locations. |
off.end |
Distance (in cM) at which to carry the genotype simulates past the p and q terminal markers on each chromosome. |
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 or Carter-Falconer map function when converting genetic distances into recombination fractions. |
After performing the forward-backward equations, we draw from Pr(g_1 = v | O) and then Pr(g_{i+1} = v | O, g_i = 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.
Calculations are done within the C function sim_geno.
Attributes "error.prob", "step", and "off.end" are set to the values of the corresponding arguments, for later reference.
The cross object in the input 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.
Karl W Broman, kbroman@jhsph.edu
http://biosun01.biostat.jhsph.edu/~kbroman/software/qtl.html
data(fake.f2) fake.f2 <- sim.geno(fake.f2,step=2,off.end=5)