modify.rf.2pts {onemap} | R Documentation |
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.
modify.rf.2pts(w, LOD = NULL, max.rf = NULL, verbose = TRUE)
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. |
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.
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. |
The thresholds used for LOD
and max.rf
will be used in
subsequent analyses.
Gabriel R A Margarido, gramarga@esalq.usp.br
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.
est.rf.2pts
,
arbitr.rf.2pts
and cr2pts
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