onemap (version 0.1-1)

make.map: Manually define a genetic map

Description

Allows the user to manually define a genetic map, i.e., a set of ordered markers on a linkage group. Genetic distances are drawn from two-point analyses.

Usage

make.map(w, ordered.group = NULL)

Arguments

w

an object of class rf.2pts, which contains the results of two-point analyses.

ordered.group

a vector of character strings indicating the names of the ordered markers, according to the original input file. The order of input of markers corresponds to the genetic map.

Value

• An object of class map, which is a list with the following components:
• order
  a numeric vector with the arbitrarily given order of genetic markers.
• recomb
  a (symmetric) matrix with two-point estimates of the recombination fraction between markers, for all pairs of markers in the linkage group, under the most probable assignment for each pair.
• marnames
  names of markers present in the linkage group, according to the original input file.
• number
  number of the linkage group. In this case, the value is -1 to indicate that the genetic map was arbitrarily defined.
• name
  name of the object of class group from where the linkage group was extracted. In this case, the value is "".
• LOD
  minimum LOD Score to declare linkage. In this case, the value is -1 to indicate that the genetic map was arbitrarily defined.
• max.rf
  maximum recombination fraction to declare linkage. In this case, the value is -1 to indicate that the genetic map was arbitrarily defined.
• phases
  a (symmetric) matrix with the most probable linkage phase (assignment) between markers, for each pair of markers in the linkage group.

References

Wu, R., Ma, C.-X., Painter, I. and Zeng, Z.-B. (2002) Simultaneous maximum likelihood estimation of linkage and linkage phases in outcrossing species. Theoretical Population Biology 61: 349-363.

See Also

map, print.map

Examples

data(example_out)
  twopts <- est.rf.2pts(example_out)
  
  my_map <- c("M18","M8","M13","M22","M7") # map for the third linkage group (details in tutorial)
  user_map <- make.map(twopts,my_map)
  user_map # must be complemented with three-point analyses