group {onemap} | R Documentation |
Identifies linkage groups of markers, using results from two-point (pairwise) analysis and the transitive property of linkage.
group(w, LOD=NULL, max.rf=NULL) ## S3 method for class 'group': print(x, detailed=TRUE, ...)
w |
an object of class sequence . |
LOD |
a (positive) real number used as minimum LOD score to declare linkage. |
max.rf |
a real number (usually smaller than 0.5) used as maximum recombination fraction to declare linkage. |
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. |
If the arguments specifying thresholds used to group markers, i.e., minimum
LOD Score and maximum recombination fraction, are NULL
(default),
the values used are those contained in object w
. If not using
NULL
, the new values overridden the ones in object w
.
Returns an object of class group
, which is a list containing
the following components:
data.name |
name of the object of class outcross that contains
the raw data. |
twopt |
name of the object of class rf.2ts used as input, i.e.,
containign information used to assign markers to linkage groups. |
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 linkage groups found. |
groups |
number of the linkage group to which each marker is assigned. |
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.
data(example_out) twopts <- rf.2pts(example_out) all.data <- make.seq(twopts,"all") link_gr <- group(all.data) link_gr