Linkage
groups are formed by assigning a marker to a group only if that marker has a recombination fraction less than or equal to this specified value with at least one marker that has already been assigned to the linkage group. If a marker is not linked to any markers in a linkage group based on this value, then that marker will be placed in a new linkage group. This value will determine the number of linkage groups.
The Minimum Spanning Tree algorithm builds a
tree
connecting markers with edges proportional to their recombination fraction (the markers with the smallest recombination values will be joined first). Once the minimum length of a potential edge between markers becomes larger than the specified threshold or the
Minimum Number of Linkage Groups
parameter value is surpassed, the algorithm will stop forming edges between markers and linkage groups will be then comprised of markers with connected edges. If you want the formation of linkage groups to be based solely on the grouping threshold specified, you should enter a value of 1 in the
Minimum Number of Linkage Groups
parameter field.
Note
: If a
Framework Linkage Group Variable
is specified, the
Minimum Number of Linkage Groups
is automatically set to the number of defined framework groups.
|
Make sure that the
Minimum Recombination Grouping
option is selected in the
Choose a linkage grouping method
parameter.
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Refer to the
SAS PROC TREE documentation
for more information.