list of crossover locations (in microns) for each of several oocytes or spermatocytes.
sclength
vector of SC lengths (in microns).
centromeres
vector of centromere locations (in microns). If missing, taken to be sclength/2.
group
nominal vector of groups; the intensity function of
the crossover process will be estimated separately for each group,
but a joint coincidence function will be estimated.
intwindow
Window size used to smooth the estimated intensity
function.
coiwindow
Window size used to smooth the estimated
coincidence function.
intloc
Locations at which to estimate the intensity
function, in the interval [0,1]
coiloc
Values at which the coincidence function is to be
estimated, in microns, less than max(sclength)
Details
The coincidence function is the probability of a recombination
event in both of two intervals, divided by the product of the two
intensity function for the two intervals.
We estimate this as a function of the distance between the two
intervals in microns, taking account of varying SC lengths,.
Value
A list containing the estimated coincidence (as a matrix
with two columns, micron distance and corresponding estimated
coincidence) and the estimated intensity functions (as a matrix
with length(group)+1 columns (the locations at which the
intensity functions were estimated followed by the group-specific estimates).
# simple example using data simulated with no crossover interference
ncells <- 1000
L <- 2 # chr lengths in Morgans (constant here)
nchi <- rpois(ncells, 2*L) # number of chiasmata
xoloc <- lapply(nchi, function(a) runif(a, 0, L)) # chi locations
coi <- est.coi.um(xoloc, rep(L, ncells))
# plot estimated coincidence and intensity
# (intensity is after scaling chromosome to length 1)
par(mfrow=c(2,1), las=1)
plot(coi$coincidence, type="l", lwd=2, ylim=c(0, max(coi$coincidence[,2])))
plot(coi$intensity, type="l", lwd=2, ylim=c(0, max(coi$intensity[,2])))