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:

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

Type the desired value into the text field.

Refer to the SAS PROC TREE documentation for more information.