xoi (version 0.72)

stahlLoglik: 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
)

Value

A vector of log likelihoods.

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

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.

Author

Karl W Broman,

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.

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))