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7.3 Sample lm_auto output

Run the example by typing:

 
lm_auto par15a

Results of interest from lm_auto are the probabilities of various gene ibd patterns for each marker and trait locus (in the map order).

 
Probabilities of IBD patterns
                                                                                
   Proband gamete set 1:  531 1  531 0  331 0  333 1
                                                                                
   pattern marker-1 marker-2 trt-geno marker-3 marker-4 marker-5    label
                                                                                
   1 1 1 1    .2025    .3185    .3450    .2950    .2315    .1275        0
   1 1 1 2    .1320    .1960    .2210    .1580    .1245    .0990        1
   1 1 2 1    .1595    .2120    .2630    .1610    .1390    .1090        3
   1 1 2 2    .0130    .0155    .0225    .0115    .0085    .0105        4
   1 1 2 3    .0285    .0360    .0540    .0300    .0245    .0170        5
   1 2 1 1    .0210    .0090    .0025    .0080    .0215    .0175        6
   1 2 1 2    .0620    .0330    .0120    .0750    .0800    .0725        7
   1 2 1 3    .0525    .0235    .0145    .0340    .0585    .0675        8
   1 2 2 1    .0365    .0220    .0050    .0225    .0300    .0315        9
   1 2 2 2    .0955    .0545    .0190    .0840    .1055    .1430       10
   1 2 2 3    .0455    .0240    .0055    .0285    .0480    .0620       11
   1 2 3 1    .0210    .0080    .0065    .0100    .0130    .0245       12
   1 2 3 2    .0695    .0320    .0170    .0500    .0670    .1135       13
   1 2 3 3    .0135    .0025    .0035    .0095    .0080    .0125       14
   1 2 3 4    .0475    .0135    .0090    .0230    .0405    .0925       15

Interpretation of these results is similar to that of ibddrop See Sample ibddrop output.

The probabilities are summarized by ibd "pattern". A pattern is a series of integers with the same length as the number of gametes to score. Same numbers indicate gametes that are ibd. For instance, `1 1 1 1' means all four gametes are ibd; `1 2 1 1' means gametes 1, 3, and 4 are ibd while gamete 2 is not ibd with the others; `1 2 3 4' means all four gametes are not ibd.

The ibd patterns are scored for each locus separately (the different columns in the table above).

Scoring selected patterns of ibd for a moving window over adjacent loci is an option:

 
Probabilities of IBD for pattern set for windows of 3 loci
                                                                                
   Proband gamete set 1:  5v1 0  5v1 1
                                                                                
   Pattern set:   0  4
                                                                                
     IBD  wndw 1 wndw 2 wndw 3 wndw 4
                                                                                
   0 0 0   .5400  .4905  .4825  .5710
   0 0 1   .0740  .0865  .0530  .0465
   0 1 0   .0305  .0405  .0450  .0530
   0 1 1   .1400  .0485  .0520  .0230
   1 0 0   .0370  .0450  .1350  .1260
   1 0 1   .0150  .0105  .0230  .0165
   1 1 0   .0250  .1175  .0975  .1120
   1 1 1   .1385  .1610  .1120  .0520

We selected ibd patterns `1 1 1 1' and `1 1 2 2', which were labeled `0' and `4' in the table of ibd probabilities. With the six loci, a window width of 3 gives us four windows for the joint scoring of the patterns.


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