search

eveilyeverafter / HMMancestry

R package using the Forward-Backward algorithm to infer genotypes, recombination hotspots, and gene conversion tracts from low-coverage next-generation sequence data.
1 stars 0 forks source link

Choice of Haldane or Kosambi mapping functions #18

Closed eveilyeverafter closed 9 years ago

eveilyeverafter commented 9 years ago

It would be nice to give the user the choice between mapping functions. Right now we just use the Haldane function:

r = 0.5*(1-e^(-2d)), where r is recombination rate between two snps and d is the mapping distance (which is the physical distance between snps times the scaling factor).

The Kosambi mapping function has the benefit taking into account crossover interference and is calculated as:

r = ((e^(4d))-1)/(2*((e^(-4d))+1))

eveilyeverafter commented 9 years ago

Opps, the paper I was referencing the Kosambi equation was wrong. The correct formula is:

r = (0.5)_(((exp(4_d))-1)/((exp(4*d))+1))