Smooth a genetic map by mixing it with a bit of constant
recombination (using a separate recombination rate for each
chromosome), to eliminate intervals that have exactly 0
recombination.
Usage
smooth_gmap(gmap, pmap, alpha = 0.02)
Value
A genetic map like the input gmap, but smoothed by mixing
it with a proportion alpha of constant recombination on each
chromosome.
Arguments
gmap
Genetic map, as a list of numeric vectors; each vector gives marker
positions for a single chromosome.
pmap
Physical map, as a list of numeric vectors; each vector gives marker
positions for a single chromosome, with the same chromosomes and markers as gmap.
alpha
Proportion of mixture to take from constant recombination.
Details
An interval of genetic length \(d_g\) and physical
length \(d_p\) is changed to have length
\((1-\alpha)d_g + \alpha d_p r\)
where \(r = L_g / L_p\) is the chromosome-specific
recombination rate.