onemap (version 0.1-1)

arbitr.rf.2pts: Arbitrarily define the linkage phase between two markers

Description

Superimposes the most probable linkage phase determined by the software with an ad hoc value chosen by the user, for any two markers in an object of class rf.2pts.

Usage

arbitr.rf.2pts(w, mrk1name = NULL, mrk2name = NULL, new.phase = NULL)

Arguments

w

an object of class rf.2pts.

mrk1name

a character string indicating the name of the first marker, corresponding to any marker in the input file used for the two-point analyses stored in object w.

mrk2name

a character string indicating the name of the second marker.

new.phase

a character string indicating the new linkage phase to be assigned between the two markers. Possible values are (Wu et al., 2002): "A1" for coupling/coupling; "A2" for coupling/repulsion; "A3"

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.
• segr.type
  a vector with the segregation type of each marker.

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

est.rf.2pts, print.rf.2pts, modify.rf.2pts and cr2pts

Examples

data(example_out)

  twopts <- est.rf.2pts(example_out)
  print(twopts,"M1","M2")
  
  # these arbitrary definitions are likely to be unnecessary
  twopts <- arbitr.rf.2pts(twopts,"M1","M2","A3") # repulsion/coupling
  print(twopts,"M1","M2")

  twopts <- arbitr.rf.2pts(twopts,"M1","M2","ns") # non-significant
  print(twopts,"M1","M2")

  twopts <- arbitr.rf.2pts(twopts,"M1","M2","A1") # back to coupling/coupling
  print(twopts,"M1","M2")