Choice of Haldane or Kosambi mapping functions
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eveilyeverafter commented
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
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))