
Identifies linkage groups of markers, using results from two-point (pairwise) analysis and the transitive property of linkage.
group(input.seq, LOD = NULL, max.rf = NULL, verbose = TRUE)
an object of class sequence
.
a (positive) real number used as minimum LOD score (threshold) to declare linkage.
a real number (usually smaller than 0.5) used as maximum recombination fraction to declare linkage.
logical. If TRUE
, current progress is shown;
if FALSE
, no output is produced.
Returns an object of class group
, which is a list
containing the following components:
name of
the object of class onemap
that contains the raw
data.
name of the object of class rf.2ts
used as input, i.e., containing information used to assign
markers to linkage groups.
marker names, according to the input file.
total number of markers.
minimum LOD Score to declare linkage.
maximum recombination fraction to declare linkage.
number of linkage groups found.
number of the linkage group to which each marker is assigned.
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 input.seq
. If not
using NULL
, the new values override the ones in object
input.seq
.
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.
# NOT RUN {
data(example_out)
twopts <- rf_2pts(example_out)
all.data <- make_seq(twopts,"all")
link_gr <- group(all.data)
link_gr
print(link_gr, details=FALSE) #omit the names of the markers
# }
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