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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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