Processes | Genetics | Framework Linkage Group Variable
Framework Linkage Group Variable
Use this field to specify an annotation variable containing values of known linkage groups for certain markers in the Input SAS Data Set . This variable will define a known framework of linkage groups.
When this variable is specified, the Minimum Recombination Grouping method (specified using the Choose a linkage grouping method parameter) 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 matching values in the Framework Linkage Group Variable are not changed (e.g., the initial composition of markers to framework linkage groups will be retained and markers in framework groups will not be considered for joining with other groups).
Note : This variable can be specified either from the Annotation SAS Data Set or from the Framework Map Data Set . If it is specified in both places, the variable entered from the Framework Map Data Set takes precedence.
To Specify the Framework Linkage Group Variable:
*
Specify the framework map data set (or the annotation 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 variable containing values of the known linkage groups.
*
Click to add the highlighted variable to the Framework Linkage Group Variable field, as shown below:
1
If this variable is specified from the Annotation SAS Data Set (which needs to have rows with Markers that exactly match the Marker columns names), then ungrouped markers for the Framework Group variable should be coded as " . " without the quotes if the variable is numeric, or coded as a blank if the variable is character. Any other value will be 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 data set, then ungrouped markers are those that are not in the Framework Map Data Set (do not match any of the values of the Framework Marker Name Variable ) or have a missing values for the Framework Linkage Group variable.