onemap (version 0.1-1)

map: Estimate the genetic map

Description

Does soma data manipulation and calls rcd to order genetic markers on a linkage group (object of class5 extracted.group).

Usage

map(w, y, LOD = NULL, max.rf = NULL)
## S3 method for class 'map':
print(x, cumulative=FALSE, \dots)

Arguments

w

an object of class extracted group (the group to be ordered).

y

the object of class rf.2pts that was used to generate object w, i.e., that contains the results of two-point analyses.

LOD

minimum LOD Score to declare linkage. If NULL (default) the threshold already present in object y is used.

max.rf

maximum recombination fraction to declare linkage. If NULL (default) the threshold already present in object y is used.

x

an object of class map.

cumulative

logical. If FALSE (default), distances between markers are printed independently for each interval. If TRUE, cumulative distances are displayed (for compatibility purposes with softwares used to draw chromosomes).

...

further arguments, passed to other methods. Currently ignored.

Value

• An object of class map, which is a list with the following components:
• order
  a numeric vector with the estimated 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, according to the numeration in the object of class group from where the linkage group was extracted.
• name
  name of the object of class group from where the linkage group was extracted.
• LOD
  minimum LOD Score to declare linkage.
• max.rf
  maximum recombination fraction to declare linkage.
• phases
  a (symmetric) matrix with the most probable linkage phase (assignment) between markers, for each pair of markers in the linkage group.

References

Doerge, R. W. (1996) Constructing genetic maps by rapid chain delineation. Journal of Quantitative Trait Loci 2: 121-132. 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

group, extract.group, rcd, make.map

Examples

data(example_out)
  
  twopts <- est.rf.2pts(example_out)  
  link_gr <- group(twopts)
  LG1 <- extract.group(link_gr,1)

  LG1_map <- map(LG1,twopts) # order makers
  LG1_map