onemap (version 2.0-4)

def.rf.3pts: Three-point analysis of genetic markers

Description

Due to the limitations of the method, this function is defunct and kept only for historical reasons. Performs the three-point analysis for outcrosses in the way proposed by Wu et al. (2002) for a triplet of markers in a given order.

Usage

def.rf.3pts(w, mrk1name = NULL, mrk2name = NULL, mrk3name = NULL, LOD =
5, max.rf = 0.35, max.nolink = 0.55)

Arguments

w

an object of class outcross.

mrk1name

a character string indicating the name of the first marker, corresponding to any marker in the input file stored in object w.

mrk2name

a character string indicating the name of the second marker.

mrk3name

a character string indicating the name of the third marker.

LOD

minimum LOD Score to declare linkage (defaults to 5).

max.rf

maximum recombination fraction between adjacent markers to declare linkage (defaults to 0.35).

max.nolink

maximum recombination fraction between markers on the edge of the triplet to declare linkage (defaults to 0.55).

Value

An object of class rf.3pts, which is a list containing the following components:

LOD

minimum LOD Score to declare linkage.

max.rf

maximum recombination fraction between adjacent markers to declare linkage.

max.nolink

maximum recombination fraction between markers on the edge of the triplet to declare linkage.

marnames

names of the three markers.

recomb

a vector with the three-point estimates of recombination fraction between markers mrk1name - mrk2name and mrk2name - mrk3name, under the most probable assignment.

phase

a character string indicating the most probable assignment (linkage phases) for the three markers.

analysis

complete results of the three-point analysis for the triplet of markers.

goodness

a vector with character strings indicating the “goodness” of each assignment, i.e., if the LOD Score and the estimates of recombination fraction are consistent with the criteria defined. Possible values are: "****" if the test is significant, the estimates are below the thresholds and the order seems to be right; "*" if the test is significant, but some estimates are above the thresholds and/or the order seems to be wrong; "-" if the test is not significant or all estimates are above the thresholds.

flag

a number indicating if there is more than one equally probable assignment for the triplet of markers. Possible values are: 1 if positive, 0 if negative and NA if linkage is not significant.

Details

The three markers are analyzed in the order they are given as input, i.e., mrk1name - mrk2name - mrk3name.

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)

  threepts <- def.rf.3pts(example.out,"M1","M2","M14") # correct order
  threepts

  threepts <- def.rf.3pts(example.out,"M1","M14","M2") # wrong order
  threepts
# }