Grouping Recombination Fraction Threshold

Use this field to specify a threshold for the grouping value of the estimated recombination fraction when using the Minimum Recombination Grouping.

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.

To Specify the Grouping Recombination Fraction Threshold:

8

Make sure that the Minimum Recombination Grouping option is selected in the Choose a linkage grouping method parameter.

8

Type the desired value into the text field.

Refer to the SAS PROC TREE documentation for more information.