Framework Linkage Group Variable

Specify a variable containing values of known linkage groups for certain markers in the Input Genotype SAS Data Set . This variable will define a known framework of linkage groups. When this variable is specified, the Minimum Recombination Grouping Option uses a constrained optimization algorithm to add new ungrouped markers ¹ to either existing groups as defined by this variable, or to a new linkage group. Group membership for markers that have values of the Framework Linkage Group Variable are not changed (the initial composition of markers to framework linkage groups is retained and markers in framework groups are not considered for joining with other groups).

To Specify a Framework Linkage Group Variable:

Specify a Framework Map Data Set .

All of the variables in the specified data set are displayed in the Available Variables field.

Examine the list of available variables.

Highlight the desired variable.

Click

to add the highlighted variable to the Framework Linkage Group Variable field.

If this variable is specified from the Annotation SAS Data Set (which needs to have rows with markers that exactly match the marker column names), then ungrouped markers for the Framework Linkage Group Variable should be coded as " . " without the quotation marks if the variable is numeric, or coded as a blank if the variable is character. Any other value is considered a framework linkage group value. If the variable is specified from the Framework Map Data Set , which does not require the number of markers or the order of the markers to match to the Input Genotype SAS Data Set , then ungrouped markers are those that are not in the Framework Map Data Set (they do not match any of the values of the Framework Marker Name Variable ) or have missing values for the Framework Linkage Group Variable .