Recombination Fraction Cutoff

Use this field to specify a recombination fraction cutoff to define clusters or linkage groups using the TREE Procedure of SAS/STAT.

Depending on the Automated Linkage Group Clustering Method chosen, this cutoff determines the number of linkage groups and group membership for markers. For Average, Complete, or Single linkage, groups are defined at the stage in clustering when the average, maximum, or minimum recombination between clusters is less than or equal to the specified cutoff respectively.

Note: In all methods, larger cutoff values correspond to a lower number of linkage groups. Typically, an appropriate value when using Average Linkage is ~0.4, which implies that the average recombination fraction between markers in a group has to be less than or equal to 0.4. If you are using Single Linkage, a smaller threshold, such as 0.25 to 0.3, is more appropriate.

To Specify the Recombination Fraction Cutoff:

8

Make sure that the Recombination Fraction Cutoff option is selected in the Define linkage groups based on the: parameter.

8

Type the desired value into the text field.

Refer to the SAS PROC TREE documentation for more information.