stahlLoglik | R Documentation |
Calculate the log likelihood for the Stahl model for varying parameters, with data on crossover locations.
stahlLoglik(
xoloc,
chrlen = NULL,
nu,
p,
max.conv = 25,
integr.tol = 0.00000001,
max.subd = 1000,
min.subd = 10
)
xoloc |
A list of crossover locations (in cM), each component being a vector of locations for a different meiotic product. |
chrlen |
Chromosome length (in cM), either of length 1 or the same
length as |
nu |
A vector of interference parameters ( |
p |
A vector of parameter values for the proportion of crossovers from the no interference pathway. |
max.conv |
Maximum limit for summation in the convolutions to get inter-crossover distance distribution from the inter-chiasma distance distributions. This should be greater than the maximum number of chiasmata on the 4-strand bundle. |
integr.tol |
Tolerance for convergence of numerical integration. |
max.subd |
Maximum number of subdivisions in numerical integration. |
min.subd |
Minimum number of subdivisions in numerical integration. |
See Housworth and Stahl (2003) and Broman and Weber (2000) for details of the method.
If neither nu
nor p
has length 1, they both must have the same
length. If one has length 1 and the other does not, the one with length 1
is repeated so that they both have the same length.
A vector of log likelihoods.
The corresponding values of nu and p are saved as attributes.
Karl W Broman, broman@wisc.edu
Housworth, E. A. and Stahl, F. W. (2003) Crossover interference in humans. Am. J. Hum. Genet. 73, 188–197.
Broman, K. W. and Weber, J. L. (2000) Characterization of human crossover interference. Am. J. Hum. Genet. 66, 1911–1926.
qtl::fitstahl()
data(bssbsb)
xoloc <- find.breaks(bssbsb, chr=1)
loglik <- stahlLoglik(xoloc, nu=4, p=c(0.05, 0.1, 0.15))
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