onemap (version 0.1-1)

modify.rf.2pts: Update two-point analyses with new criteria

Description

Takes an object of class rf.2pts and updates the analyses with new criteria, i.e., new thresholds for LOD Score and maximum recombination fraction.

Usage

modify.rf.2pts(w, LOD = NULL, max.rf = NULL, verbose = TRUE)

Arguments

w

an object of class rf.2pts.

LOD

minimum LOD Score to declare linkage. NULL (default) indicates that the LOD Score threshold will not be changed.

max.rf

maximum recombination fraction to declare linkage. NULL (default) indicates that the maximum recombination fraction threshold will not be changed.

verbose

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

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

The two-point analyses are not re-done: the results of the former analyses are re-interpreted in light of the new criteria and a new object of class rf.2pts is produced for further investigation.

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, arbitr.rf.2pts and cr2pts

Examples

data(example_out)

  twopts <- est.rf.2pts(example_out,LOD=3,max.rf=0.35) # perform two-point analyses
  twopts

  twopts <- modify.rf.2pts(twopts,max.rf=0.5) # same LOD Score threshold, new maximum recombination fraction criterion
  twopts