bestmapfun: Best fitting genetic-map function

In hsrecombi: Estimation of Recombination Rate and Maternal LD in Half-Sibs

Best fitting genetic-map function

Description

Approximation of mixing parameter of system of map functions

Usage

bestmapfun(theta, dist_M)

Arguments

theta	vector of recombination rates
dist_M	vector of genetic positions

Details

The genetic mapping function that fits best to the genetic data (recombination rate and genetic distances) is obtained from Rao's system of genetic-map functions. The corresponding mixing parameter is estimated via 1-dimensional constrained optimisation. See vignette for its application to estimated data.

Value

list (LEN 2)

mixing

mixing parameter of system of genetic mapping functions

mse

minimum value of target function (theta - dist_M)^2

References

Rao, D.C., Morton, N.E., Lindsten, J., Hulten, M. & Yee, S (1977) A mapping function for man. Human Heredity 27: 99-104. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1159/000152856")}

Examples

  theta <- seq(0, 0.5, 0.01)
  gendist <- -log(1 - 2 * theta) / 2
  bestmapfun(theta, gendist)

hsrecombi documentation built on June 7, 2023, 6:02 p.m.