location.given.one: Location of crossover given there is one

In kbroman/xoi: Tools for Analyzing Crossover Interference

Location of crossover given there is one

Description

Calculates the density of the location of the crossover on a random meiotic product, given that there is precisely one crossover, for the gamma model.

Usage

location.given.one(
  nu,
  L = 103,
  x = NULL,
  n = 400,
  max.conv = 25,
  integr.tol = 0.00000001,
  max.subd = 1000,
  min.subd = 10
)

Arguments

nu	The interference parameter in the gamma model.
L	The length of the chromsome in cM.
x	If specified, points at which to calculate the density.
n	Number of points at which to calculate the density. The points will be evenly distributed between 0 and L. Ignored if x is specified.
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

Let f(x;\nu) denote the density of a gamma random variable with parameters shape=\nu and rate=2\nu, and let f_k(x;\nu) denote the density of a gamma random variable with parameters shape=k \nu and rate=2\nu.

The distribution of the distance from one crossover to the next is f^*(x;\nu) = \sum_{k=1}^{\infty} f_k(x;\nu)/2^k.

The distribution of the distance from the start of the chromosome to the first crossover is g^*(x;\nu) = 1 - F^*(x;\nu) where F^* is the cdf of f^*.

We calculate the distribution of the location of the crossover on a product with a single crossover as the convolution of g^* with itself, and then rescaled to integrate to 1 on the interval (0,L).

Value

A data frame with two columns: x is the location (between 0 and L, in cM) at which the density was calculated and f is the density.

Author(s)

Karl W Broman, [e-mail]

References

Broman, K. W. and Weber, J. L. (2000) Characterization of human crossover interference. Am. J. Hum. Genet. 66, 1911–1926.

Broman, K. W., Rowe, L. B., Churchill, G. A. and Paigen, K. (2002) Crossover interference in the mouse. Genetics 160, 1123–1131.

McPeek, M. S. and Speed, T. P. (1995) Modeling interference in genetic recombination. Genetics 139, 1031–1044.

See Also

first.given.two(), distance.given.two(), joint.given.two(), ioden(), firstden(), xoprob(), gammacoi()

Examples

f1 <- location.given.one(1, L=200, n=201)
plot(f1, type="l", lwd=2, las=1,
     ylim=c(0,0.006), yaxs="i", xaxs="i", xlim=c(0,200))

f2 <- location.given.one(2.6, L=200, n=201)
lines(f2, col="blue", lwd=2)

f3 <- location.given.one(4.3, L=200, n=201)
lines(f3, col="red", lwd=2)

f4 <- location.given.one(7.6, L=200, n=201)
lines(f4, col="green", lwd=2)

kbroman/xoi documentation built on May 1, 2023, 9:35 p.m.