| arbitr.rf.2pts {onemap} | R Documentation |
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.
arbitr.rf.2pts(w, mrk1name = NULL, mrk2name = NULL, new.phase = NULL)
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" for
repulsion/coupling; "A4" for repulsion/repulsion; "ns"
for not significant. |
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. |
Intended to be used if other sources of information are available. Use this function very carefully.
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, print.rf.2pts,
modify.rf.2pts and cr2pts
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")