The ALLELE Procedure

The following is a subset of data from GAW12 (Wijsman et al. 2001) and contains 17 individuals’ genotypes at 14 microsatellite markers.

data gaw;
   input id m1-m14 / m15-m28;
   datalines;
 1 11 14  6  8  2  5  9  4  6  1  9  9  9  7
    3  5 10  1  4  6  5  9  1  1  3  5  6  2   
 2  2 12  1  4  6  6  3  3  2  1 11 11  4 11  
    2  2 13 11  2  1  9  9  1  5  6  1  2  5    
 3  2 10  4  8  4  9  2  7  7  1  9  2  7 10  
    2  2  7  7  6  8  9  4  5  1  7  2  6  2   
 4  5 14  7  3  9 13  4  2  2  4 11  5  4  7  
    4  5  7  6  8  2  9  9  1  6  4  1  8  9         
 5 12 12  3  8  6  2  1  7  3  5  6 11  6  9  
    5  2 13 16  7  1  9  4  1  1  7  1  1  2   
 6  4  7  7  8  7 12  4  2  6  5  5 11  5 11  
    2  4 15 11  1  1  9  2  6  5  7  6  1  5    
 7  2 10  6  8  7  1  2  3  6  2  5  8  5  6  
    5  6 13 10  1  8  9  3  1  6  7  7  2  6    
 8  2 11  6  2  7  1  2  3  6  6 10 11 11  6  
    4  2 11 11  4  5 11  2  3  2  1  4  1  2     
 9  2  7  1  1  3  1  5  7  2  5  5 11 11 11  
    2  6 11  2  1  6  4  9  5  5  4  2  5  9     
10 11 12  2  4 13  3  1  2  4  9  5 10  7  5  
    4  4  1  6  8  1  6 10  1  1  2  5  1  1    
11 11  2  7  8  1  5  4  6  4  7  5 11 11  6  
    5  4 16 13  7  4  5  6  6  1  1  4  1  1     
12  2 12  6  8  2  7  3  2  7  5  2  8  9  6  
    2  4  7 16  7  1 10  9  5  1  1  4  9  1     
13 13 14  8  3 12 13  7  4  3  2  6 10  9  5  
    4  4  2 14  8  8  3  6  5  1  1  6  6  2    
14  7 10  6  5 10 13  8  3  5  5  9  9 11  6  
    5  4 13 14  1  1  6  9  2  1  5  3  1  2    
15 10 11  4  3  9  7  6  3  4  6 10  1  7  9  
    2  2  2 14  6  1  9  2  1  1  6  7  5  2    
16  2  5  2  7  7  2  2  9  2  2  2  6  9  5  
    2  2  7  1  1  2  6  2  1  1  1  1  9  6      
17 11  4  4  4  9  1  7  8  5  3  5  1 11  5  
    6  5  2 12  1  5  9  9  1  5  7  7  6  1    
; 

The actual names of the markers can be used, by creating a data set with the variable NAME containing these names.

data map;
   input name $ location;
   datalines;
D22G001   0.50
D22G002   0.79
D22G003   0.88
D22G004   1.02
D22G005   1.24
D22G006   2.20
D22G007   4.27
D22G008   5.85
D22G009   6.70
D22G010   9.36
D22G011  10.87
D22G012  11.67
D22G013  12.66
D22G014  15.89
;

Now an analysis using PROC ALLELE can be performed as follows:

proc allele data=gaw ndata=map nofreq perms=10000 seed=456;
   var m1-m28;
run;

This analysis produces summary statistics of the 14 markers and is using 10,000 permutations to approximate an exact -value for the HWE test. The allele and genotype frequency output tables are suppressed with the NOFREQ option.

The results from the analysis are shown in Output 3.1.1. Note the names of the markers that are used.