Filter to Select Markers for PCA

The Filter to Select Markers for PCA field is an optional parameter that enables you to specify marker variables to use for the calculation of principal components for individuals. By default, all marker variables are used in the PCA.

You can type one or more statements to select markers to use for the PCA based on variables in the annotation data set. Only markers that meet the condition(s) specified are used to compute principal components for individuals. All Marker Variables are still included in the Q-K mixed model.

Important: You still must specify all variables that correspond to the markers in the entire annotation data set as Marker Variables.

For example, to filter only diseased individuals from a data set containing a mixed population of diseased (sick) and healthy (healthy) individuals (as indicated in a column named DiseaseStatus), you could use the following simple WHERE expression:

WHERE DiseaseStatus = ‘sick’

Note: The word where has already been entered for you.

For more information about using filter fields, see The SAS WHERE Expression.