make.map {onemap}R Documentation

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.

Author(s)

Gabriel R A Margarido, gramarga@esalq.usp.br

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

[Package onemap version 0.1-1 Index]