onemap (version 0.1-0)

est.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

est.rf.2pts(w, LOD = 3, max.rf = 0.35, verbose = TRUE)
## S3 method for class 'rf.2pts':
print(x, mrk1 = NULL, mrk2 = NULL, \dots)

Arguments

w

an object of class outcross.

LOD

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

max.rf

maximum recombination fraction to declare linkage (defaults to 0.35).

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 inpu

...

further arguments, passed to other methods. Currently ignored.

Value

• An object of class rf.2pts, which is a list containing the following components:
• n.mar
  total number of markers.
• LOD
  minimum LOD Score to declare linkage.
• max.rf
  maximum recombination fraction to declare linkage.
• recomb
  a (symmetric) matrix with two-point estimates of the recombination fraction between markers (for all pairs of markers), under the most probable assignment for each pair.
• phases
  a (symmetric) matrix with the most probable linkage phase (assignment) between markers, for each pair of markers.
• analysis
  an array with the complete results of the two-point analysis for each pair of markers.
• flags
  a (symmetric) matrix indicating if there is more than one equally probable linkage phase for each pair of markers. Possible values are: 1 if positive, 0 if negative and NA if linkage is not significant.
• arbitr
  a (symmetric) matrix indicating the most probable linkage phase for each pair of markers, when arbitrarily defined by the user. This function will actually return a matrix filled with zeroes, which indicates that the linkage phases were determined by the software (but may be arbitrarily changed afterwards).
• segr.type
  a vector with the segregation type of each marker.

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 quite 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.

See Also

modify.rf.2pts to modify criteria used in the analyses; arbitr.rf.2pts and cr2pts

Examples

data(example_out)

  twopts <- est.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