An Eigenvalue test for spatial principal component analysis

Montano, V.; Jombart, T.

doi:10.1186/s12859-017-1988-y

BMC Bioinformatics

Table 2 Results for the same simulations reported in Table 1 using a subset of 40 loci per individual

From: An Eigenvalue test for spatial principal component analysis

40 SNPs		Random Patterns				Global Patterns				Local Patterns
Models	Significance level	g test	r test (+)	l test	r test (−)	g test	r test (+)	l test	r test (−)	g test	r test (+)	l test	r test (−)
IS-1	.05	0.052	0.061	0.046	0.050	0.591	0.807	0.033	0.004	0.036	0.000	0.055	0.077
	.01	0.016	0.013	0.010	0.007	0.393	0.592	0.005	0.000	0.004	0.000	0.015	0.022
IS-2	.05	0.053	0.047	0.038	0.042	0.103	0.226	0.046	0.020	0.073	0.000	0.057	0.038
	.01	0.011	0.009	0.006	0.006	0.022	0.072	0.011	0.005	0.012	0.000	0.010	0.006
IS-3	.05	0.047	0.050	0.050	0.045	0.048	0.060	0.044	0.042	0.036	0.000	0.053	0.026
	.01	0.009	0.011	0.008	0.007	0.009	0.011	0.011	0.011	0.002	0.000	0.013	0.001
SS-1	.05	0.052	0.054	0.039	0.049	0.898	0.949	0.017	0.000	0.050	0.001	0.067	0.169
	.01	0.009	0.012	0.005	0.011	0.826	0.865	0.006	0.000	0.007	0.000	0.021	0.052
SS-2	.05	0.046	0.045	0.050	0.046	0.528	0.588	0.044	0.009	0.052	0.000	0.048	0.081
	.01	0.013	0.010	0.010	0.015	0.377	0.370	0.016	0.000	0.005	0.000	0.011	0.014
SS-3	.05	0.068	0.040	0.050	0.048	0.066	0.055	0.053	0.033	0.026	0.000	0.047	0.023
	.01	0.014	0.005	0.013	0.012	0.012	0.009	0.005	0.006	0.006	0.000	0.008	0.000
IBD-1	.05	0.049	0.053	0.052	0.057	0.822	0.883	0.027	0.002	0.034	0.055	0.124	0.480
	.01	0.005	0.008	0.013	0.013	0.755	0.742	0.004	0.000	0.005	0.008	0.032	0.278
IBD-2	.05	0.043	0.054	0.060	0.049	0.835	0.880	0.028	0.001	0.043	0.051	0.111	0.458
	.01	0.011	0.007	0.015	0.009	0.755	0.732	0.005	0.000	0.008	0.015	0.026	0.259
IBD-3	.05	0.043	0.042	0.051	0.050	0.844	0.899	0.026	0.002	0.048	0.058	0.115	0.465
	.01	0.012	0.013	0.012	0.010	0.763	0.756	0.007	0.000	0.009	0.010	0.023	0.263

* p-values are in italic when non significant and in bold when the fraction of true positive is above 20%

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ISSN: 1471-2105

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