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")