map_func: Mapping functions Haldane and Kosambi

In BatchMap: Software for the Creation of High Density Linkage Maps in Outcrossing Species

Description

Functions to convert recombination fractions to distance in cM (centiMorgans).

Usage

haldane(rcmb)
kosambi(rcmb)

Arguments

rcmb	A recombination fraction between two markers, i.e., a number between 0 and 0.5.

Details

Haldane mapping function is defined as

dM = -(1/2) ln(1-2r),

for 0 ≤q r ≤q 0.5, where r stands for the recombination fraction in rcmb. Kosambi mapping function is

dM = (1/4) ln [(1+2r)/(1-2r),

for 0 ≤q r ≤q 0.5, where r is defined as above.

Value

Both functions return a number with a distance measured in cM.

Author(s)

Gabriel R A Margarido, [e-mail]

References

Haldane, J. B. S. (1919) The combination of linkage values and the calculation of distance between the loci of linked factors. Journal of Genetics 8: 299-309.

Kosambi, D. D. (1944) The estimation of map distance from recombination values. Annuaire of Eugenetics 12: 172-175.

Examples

  # little difference for small recombination fractions
  haldane(0.05)
  kosambi(0.05)

  # greater difference as recombination fraction increases
  haldane(0.35)
  kosambi(0.35)

Example output

Loading required package: parallel
Loading required package: ggplot2
[1] 5.268026
[1] 5.016767
[1] 60.19864
[1] 43.36503

BatchMap documentation built on May 2, 2019, 3:45 p.m.