stahlLoglik {xoi}

Calculate log likelihood for Stahl model

Description

Calculate the log likelihood for the Stahl model for varying parameters, with data on crossover locations.

Usage

stahlLoglik(
  xoloc,
  chrlen = NULL,
  nu,
  p,
  max.conv = 25,
  integr.tol = 0.00000001,
  max.subd = 1000,
  min.subd = 10
)

Arguments

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 xoloc.

nu

A vector of interference parameters (\nu) at which to calculate the log likelihood.

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.

Details

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.

Value

A vector of log likelihoods.

The corresponding values of nu and p are saved as attributes.

Author(s)

Karl W Broman, [e-mail]

References

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.

See Also

qtl::fitstahl()

Examples

data(bssbsb)
xoloc <- find.breaks(bssbsb, chr=1)

loglik <- stahlLoglik(xoloc, nu=4, p=c(0.05, 0.1, 0.15))