10.3 Sample lm_ibdtests output

Under the subdirectory `TraitTests/', run the example with the following command

./lm_ibdtests ped73_ibdt_IBD.par

The part of the output that tabulates test statistics and p values is shown below. The upper table provides the permutation-test p-values for each of the two test statistics Spairs and Srobdom at each of the 10 marker-locus positions, these positions being given for both the male and female genetic maps. It is apparent that there is no significant association of the trait with any of these marker positions; the p-values at markers 5 and 6 are somewhat smaller, but do not achieve (e.g.) a 0.05 significance level. The lower table gives the same result, but this time using a Normal distribution approximation to obtain the p-value. In this case the standardized (N(0,1)) value of the test statistic is given, as well as the corresponding p-value. Again there are no significant results in this small example. There is a broad qualitative correspondence between the p-values of the two tables, but the results are not close. This may be due to the small number of permutations used, or, more likely, due to the inadequacies of the Normal approximation.

************************************ p Value for Permutation Test for IBD ************************************ pos(Haldane cM) Spairs Srobdom locus male female p-value p-value marker-1 0.000 0.000 0.9020 0.9300 marker-2 10.000 10.000 0.8780 0.8450 marker-3 20.000 20.000 0.8130 0.7800 marker-4 30.000 30.000 0.5080 0.5190 marker-5 40.000 40.000 0.2550 0.2480 marker-6 50.000 50.000 0.2950 0.2510 marker-7 60.000 60.000 0.3850 0.5090 marker-8 70.000 70.000 0.5100 0.6660 marker-9 80.000 80.000 0.6610 0.7750 marker-10 90.000 90.000 0.5640 0.7470 ******************************* p Value for Normal Test for IBD ******************************* pos(Haldane cM) locus male female Spairs p-value Srobdom p-value marker-1 0.000 0.000 -0.7843 0.7951 -0.2867 0.6167 marker-2 10.000 10.000 -0.9574 0.8166 -0.3841 0.6567 marker-3 20.000 20.000 -1.1825 0.8816 -0.2260 0.5692 marker-4 30.000 30.000 -0.6437 0.7381 -0.1272 0.5552 marker-5 40.000 40.000 0.2478 0.4103 0.0986 0.4743 marker-6 50.000 50.000 -0.2270 0.5752 -0.3275 0.6252 marker-7 60.000 60.000 -0.1503 0.5612 -0.3514 0.6437 marker-8 70.000 70.000 -0.3096 0.6372 -0.3587 0.6557 marker-9 80.000 80.000 -0.4877 0.6902 -0.2706 0.6037 marker-10 90.000 90.000 -0.2924 0.6222 -0.1136 0.5662

Your values may be different due to different random seed files.

For more details about the lm_ibdtest methods see Basu et al. (2008) Annals of Human Genetics 72: 676-682.