ALLELE Procedure

The new POP statement enables you to specify a variable that defines populations. Various statistics can be computed that serve to describe the genetic structure of the population hierarchy.

The MAXDIST= option of the PROC ALLELE statement can now be specified in terms of the unit used to define markers’ locations. A LOCATION variable can be included in the NDATA= data set, containing a numeric value that represents each marker’s location, and the MAXDIST= option is applied to the distance between markers (the absolute value of the difference of the two LOCATION values) for determining whether linkage disequilibrium (LD) measures are to be calculated for that particular pair. When the NDATA= option is not specified or the data set does not contain a LOCATION variable, the MAXDIST= option functions as it did previously, calculating the distance between markers as the number of markers apart they are.

The upper bound for the LD measure , used in the denominator of the measure, is now calculated according to Hamilton and Cole (2004) and Zaykin (2004) when HAPLO=NONE or NONEHWD.

The new RHO option in the PROC ALLELE statement requests that the LD measure and its information (Morton et al. 2001) be included in the "Linkage Disequilibrium Measures" table. This table now also includes a column containing the number of individuals genotyped at each pair of markers.