feat_recombination: Feature: Recombination
This feature adds intra-locus recombination to a model. The rate is per locus
for unlinked loci and per trio for linked
locus trios. By default, the same recombination rate is used
for all loci, but it is possible to change this with
par_zero_inflation. Coala assumes that recombination events
can occur between all neighboring bases.
(rate, locus_group = "all")
The recombination rate. Can be a numeric or a
parameter. The rate is equal to
4*N0*r, where r is the probability that a
recombination event within the locus occurs in one generation.
The loci for which this features is used. Can either be
"all" (default), in which case the feature is used for simulating
all loci, or a numeric vector. In the latter case, the feature is only
used for the loci added in
locus_ commands with the corresponding
index starting from 1 in order in which the commands where added to the
model. For example, if a model has
locus_single(10) + locus_averaged(10, 11) + locus_single(12) and
this argument is
c(2, 3), than the feature is used for all but
the first locus (that is locus 2 - 12).
The feature, which can be added to a model using '+'.
The feature, which can be added to a model created with
For creating a model:
For adding recombination:
# Simulate a 1.5kb sequence for 10 individuals with recombination:
model <- (10, 2, 1500) +