onemap (version 2.0-4)

rf.2pts: Two-point analysis between genetic markers

Description

Performs the two-point (pairwise) analysis proposed by Wu et al. (2002) between all pairs of markers.

Usage

rf.2pts(input.obj, LOD = 3, max.rf = 0.50, verbose = TRUE)
# S3 method for rf.2pts
print(x, mrk1 = NULL, mrk2 = NULL, …)

Arguments

input.obj

an object of class outcross, bc.onemap, f2.onemap, riself.onemap or risib.onemap.

LOD

minimum LOD Score to declare linkage (defaults to 3).

max.rf

maximum recombination fraction to declare linkage (defaults to 0.50).

verbose

logical. If TRUE, current progress is shown; if FALSE, no output is produced.

x

an object of class rf.2pts.

mrk1, mrk2

optionally, two markers can be specified. If so, detailed results of the two-point analysis will be printed for this pair. Both arguments can be numeric or character strings indicating the numbers/names corresponding to any markers in the input file.

…

further arguments, passed to other methods. Currently ignored.

Value

An object of class rf.2pts, which is a list containing the following components:

data.name

name of the object with the raw data.

n.mar

total number of markers.

marnames

marker names, according to the input file.

LOD

minimum LOD Score to declare linkage.

max.rf

maximum recombination fraction to declare linkage.

input

the name of the input file.

analysis

an array with the complete results of the two-point analysis for each pair of markers.

Details

For n markers, there are $$\frac{n(n-1)}{2}$$ pairs of markers to be analyzed. Therefore, completion of the two-point analyses can take a long time.

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.

Examples

# NOT RUN {
  data(example.out)

  twopts <- rf.2pts(example.out,LOD=3,max.rf=0.5) # perform two-point analyses
  twopts

  print(twopts,"M1","M2") # detailed results for markers 1 and 2
# }