
Calculates the density of the distance from a given crossover to the next crossover, for the gamma model.
ioden(nu, L = 103, x = NULL, n = 400, max.conv = 25)
A data frame with two columns: x
is the distance (between 0
and L
, in cM) at which the density was calculated and f
is the
density.
The interference parameter in the gamma model.
Maximal distance (in cM) at which to calculate the density. Ignored
if x
is specified.
If specified, points at which to calculate the density.
Number of points at which to calculate the density. The points
will be evenly distributed between 0 and L
. Ignored if x
is
specified.
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.
Karl W Broman, broman@wisc.edu
Let
The distribution of the distance from one crossover to the next is
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.
location.given.one()
, first.given.two()
,
distance.given.two()
, joint.given.two()
,
firstden()
, xoprob()
, gammacoi()
f1 <- ioden(1, L=200, n=201)
plot(f1, type="l", lwd=2, las=1,
ylim=c(0,0.014), yaxs="i", xaxs="i", xlim=c(0,200))
f2 <- ioden(2.6, L=200, n=201)
lines(f2, col="blue", lwd=2)
f3 <- ioden(4.3, L=200, n=201)
lines(f3, col="red", lwd=2)
f4 <- ioden(7.6, L=200, n=201)
lines(f4, col="green", lwd=2)
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