| formLinkageGroups {qtl} | R Documentation |
Use pairwise linkage information between markers (as calculated by
est.rf to partition markers into linkage groups.
formLinkageGroups(cross, max.rf=0.25, min.lod=3, reorgMarkers=FALSE,
verbose=FALSE)
cross |
An object of class cross. See
read.cross for details. |
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. |
Two markers are placed in the same linkage group if the estimated
recombination fraction between them is <= max.rf and
the LOD score (for the test of the rec. frac. = 1/2) is >=
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.
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.
Karl W Broman, kbroman@biostat.wisc.edu
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))