Specify a threshold for the grouping value of the estimated recombination fraction when using
Minimum Recombination Grouping
. Linkage groups are formed by assigning a marker to a group
only
if the marker has a recombination fraction
less than or equal to
this specified value with at least one marker already in the
linkage
group. If a marker is
not
linked to any markers in a linkage group based on this value, then that marker is placed in a new linkage group. This value determines 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 are 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
value (equal to the number of framework groups when
Minimum Recombination Grouping
is used only with a framework) is surpassed, the algorithm stops forming edges between markers, and linkage groups are then comprised of markers with connected edges.
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.
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