est.rf.2pts {onemap} | R Documentation |
Performs the two-point (pairwise) analysis proposed by Wu et al. (2002) between all pairs of markers.
est.rf.2pts(w, LOD = 3, max.rf = 0.35, verbose = TRUE) ## S3 method for class 'rf.2pts': print(x, mrk1 = NULL, mrk2 = NULL, ...)
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 input file. |
... |
further arguments, passed to other methods. Currently ignored. |
For n
markers, there are
n*(n-1)/2
pairs of markers to be analyzed. Therefore, completion of the two-point analyses can take quite a long time.
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.
modify.rf.2pts
to modify criteria used in the
analyses; arbitr.rf.2pts
and
cr2pts
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