formLinkageGroups {qtl} | R Documentation |
Partition markers into linkage groups
Description
Use pairwise linkage information between markers (as calculated by
est.rf
to partition markers into linkage groups.
Usage
formLinkageGroups(cross, max.rf=0.25, min.lod=3, reorgMarkers=FALSE,
verbose=FALSE)
Arguments
cross |
An object of class |
max.rf |
Maximum recombination fraction for placing two markers in the same linkage group (see Details). |
min.lod |
Minimum LOD score for placing two markers in the same linkage group (see Details). |
reorgMarkers |
If TRUE, the output is a cross object, like the input, but with the markers organized into the inferred linkage groups. If FALSE, the output is a table indicating the initial chromosome assignments and the inferred linkage group partitions. |
verbose |
If TRUE, display information about the progress of the calculations. |
Details
Two markers are placed in the same linkage group if the estimated
recombination fraction between them is \le
max.rf
and
the LOD score (for the test of the rec. frac. = 1/2) is \ge
min.lod
. The transitive property (if A is linked to B and B is
linked to C then A is linked to C) is used to close the groups.
Value
If reorgMarkers=FALSE
(the default), the output is a data frame
with rows corresponding to the markers and with two columns: the
initial chromosome assignment and the inferred linkage group. Linkage
groups are ordered by the number of markers they contain (from largest
to smallest).
If reorgMarkers=TRUE
, the output is a cross object, like the
input, but with the markers reorganized into the inferred linkage
groups. The marker order and marker positions within the linkage
groups are arbitrary.
Author(s)
Karl W Broman, broman@wisc.edu
See Also
Examples
data(listeria)
listeria <- est.rf(listeria)
result <- formLinkageGroups(listeria)
tab <- table(result[,1], result[,2])
apply(tab, 1, function(a) sum(a!=0))
apply(tab, 2, function(a) sum(a!=0))