group {onemap} | R Documentation |
Identifies linkage groups of markers, using results from two-point (pairwise) analysis and the transitive property of linkage.
group(w) ## S3 method for class 'group': print(x, detailed=TRUE, ...)
w |
an object of class rf.2pts . |
x |
an object of class group . |
detailed |
logical. If FALSE , only a small summary of the
linkage groups is printed. If TRUE (default), the names of
markers in each linkage group are also displayed. |
... |
further arguments, passed to other methods. Currently ignored. |
Thresholds used to group markers, i.e., minimum LOD Score and maximum
recombination fraction, are defined in object w
.
Returns an object of class group
, which is a list containing
the following components:
marnames |
marker names, according to the input file. |
n.mar |
total number of markers. |
LOD |
minimum LOD Score to declare linkage. |
max.rf |
maximum recombination fraction to declare linkage. |
n.groups |
number of groups found. |
groups |
number of the linkage group to which each marker is assigned. |
name |
name of the object of class rf.2pts used as input,
i.e., containing the information used to assign markers to linkage
groups. |
Gabriel R A Margarido, gramarga@esalq.usp.br
Lincoln, S. E., Daly, M. J. and Lander, E. S. (1993) Constructing genetic linkage maps with MAPMAKER/EXP Version 3.0: a tutorial and reference manual. A Whitehead Institute for Biomedical Research Technical Report.
est.rf.2pts
,
modify.rf.2pts
and
arbitr.rf.2pts
data(example_out) twopts <- est.rf.2pts(example_out) link_gr <- group(twopts) link_gr