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lm_auto example and sample output Under the subdirectory `IBD/', run the example by typing:
lm_auto jv_rep_auto.par > auto.out |
Below are sections of the output file `auto.out', generated by
running lm_auto using the parameter file `jv_rep_auto.par'.
The first table gives probabilities of
gene ibd patterns for each marker and the 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 .1985 .2960 .3480 .2920 .2430 .1840 0
1 1 1 2 .1400 .2280 .2690 .2205 .1720 .1145 1
1 1 2 1 .1265 .1495 .2050 .1225 .0975 .0985 3
1 1 2 2 .0145 .0165 .0200 .0145 .0125 .0070 4
1 1 2 3 .0340 .0350 .0515 .0255 .0220 .0130 5
1 2 1 1 .0235 .0150 .0030 .0095 .0185 .0275 6
1 2 1 2 .0755 .0425 .0110 .0640 .0705 .0775 7
1 2 1 3 .0595 .0330 .0085 .0310 .0515 .0570 8
1 2 2 1 .0380 .0260 .0030 .0275 .0300 .0435 9
1 2 2 2 .1035 .0605 .0255 .0860 .1175 .1530 10
1 2 2 3 .0540 .0370 .0150 .0385 .0490 .0580 11
1 2 3 1 .0200 .0080 .0035 .0060 .0140 .0210 12
1 2 3 2 .0495 .0255 .0155 .0385 .0645 .0700 13
1 2 3 3 .0100 .0045 .0060 .0030 .0095 .0170 14
1 2 3 4 .0530 .0230 .0155 .0210 .0280 .0585 15
Probabilities of IBD for pattern set for windows of 3 loci
Proband gamete set 1
Pattern set: 0 4
IBD wndw 1 wndw 2 wndw 3 wndw 4
0 0 0 .5325 .4900 .4740 .5385
0 0 1 .0975 .0870 .0625 .0685
0 1 0 .0295 .0440 .0400 .0550
0 1 1 .1275 .0665 .0555 .0315
1 0 0 .0445 .0465 .1330 .1125
1 0 1 .0130 .0085 .0240 .0250
1 1 0 .0255 .1130 .0975 .1030
1 1 1 .1300 .1445 .1135 .0660
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Interpretation of these results is similar to that of ibddrop
See Running ibddrop example and sample output. Briefly, the probabilities are summarized
by ibd pattern. A pattern is a series of integers, one
representing each gamete listed in the `set proband gametes'
statement. The order of gametes in the output file patterns is the same
as the order in which the gametes were listed in `set proband
gametes'. Numbers that are the same indicate gametes that are ibd.
For instance, in the first row of the table above, the pattern is
`1 1 1 1', which means that the values in row one represent
probabilities that all four gametes are ibd at each marker locus and
at the trait locus. Likewise, `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 second table in the above output is due to the window size and ibd
pattern statements in the parameter file. Its interpretation is similar
to the output of ibddrop when statement `set locus window'
was used, See Running ibddrop example and sample output. In
ibddrop, the values in the `IBD' column of the output
indicate whether the gametes specified in the `set proband gametes'
statement are all ibd (indicated by a `1') or if at least one
of the gametes is not ibd with the others (indicated by a `0').
With lm_auto, the user can specify additional ibd patterns of
interest. In this example, the parameter file `jv_rep_auto.par' includes
the statement `set window patterns 0 4', indicating that we are
interested in ibd patterns `0' and `4', corresponding to
`1 1 1 1' and `1 1 2 2', respectively, as discussed in the
previous section. That is, we would like to know the probability that
either all four gametes are ibd or that the first two are ibd
and the second two are ibd, but the pairs are not ibd with one
another for each window of three loci. Consequently, interpretation of
the `IBD' column of the lm_auto output is as follows. The
row headed by `0 0 0' gives probabilities that the gametes do not
follow either of the two ibd patterns of interest at all three loci
for each window. The row headed by `0 0 1' gives probabilities
that the gametes do not follow either of the two ibd patterns of
interest at the first two loci in the window, but at the third loci
either all four gametes are ibd or the first two are ibd and
the last two are ibd, but the pairs are not ibd with one
another.
In this section of the lm_auto output, the order of the marker
and trait loci is the same as above. In this example, the trait locus
was between markers 2 and 3. Therefore, the windows are as below:
window
wndw 1
wndw 2
wndw 3
wndw 4
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