est.rf.3pts {onemap} | R Documentation |
Performs the three-point analysis proposed by Wu et al. (2002) for a triplet of markers in a given order.
est.rf.3pts(w, mrk1name = NULL, mrk2name = NULL, mrk3name = NULL, LOD = 5, max.rf = 0.35, max.nolink = 0.55)
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 ). |
The three markers are analyzed in the order they are given as input,
i.e., mrk1name - mrk2name - mrk3name
.
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. |
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.
data(example_out) threepts <- est.rf.3pts(example_out,"M1","M2","M14") # correct order threepts threepts <- est.rf.3pts(example_out,"M1","M14","M2") # wrong order threepts