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FilenameFormatSizeDescription
gepi21715-sup-0001-FigureS1.pdf51KFigure S1. Comparisons of p-values from perturbation vs. permutation for sample sizes of 250 and 500.
gepi21715-sup-0002-Tables.pdf59K

Table S1: Absolute power simulation results based on the four configurations for continuous trait values. Linear, IBS, and Quadratic correspond to the linear, IBS, and quadratic kernels. Average corresponds to using the composite kernel generated as the average of the linear, IBS, and quadratic kernel. Perturb denotes the proposed perturbation procedure using all three candidate kernels.

Table S2: Relative power simulation results based on the four configurations for dichotomous trait values. Linear, IBS, and Quadratic correspond to the linear, IBS, and quadratic kernels. Average corresponds to using the composite kernel generated as the average of the linear, IBS, and quadratic kernel. Perturb denotes the proposed perturbation procedure using all three candidate kernels. Power is expressed as the power relative to the best (of the three individual kernels). Also included are the power comparisons with two competing approaches for multi-SNP analysis using the PCA or minimum p-value methods.

Table S3: Absolute power simulation results based on the four configurations for dichotomous trait values. Linear, IBS, and Quadratic correspond to the linear, IBS, and quadratic kernels. Average corresponds to using the composite kernel generated as the average of the linear, IBS, and quadratic kernel. Perturb denotes the proposed perturba- tion procedure using all three candidate kernels. Also included are the power comparisons with two competing approaches for multi-SNP analysis using the PCA or minimum p-value methods.

Table S5: Pre-term Birth Data Analysis Results. Each number represents the number of SNP sets called significant at the FDR = 0.10 level by both the method along the top and the side of the table. Diagonal elements represent the number of SNP sets called significant by each individual method.

Table 6: Pre-term Birth Data Analysis Results. Each number represents the number of SNP sets called significant at the FDR = 0.25 level by both the method along the top and the side of the table. Diagonal elements represent the number of SNP sets called significant by each individual method.

Table S7: Pre-term Birth Data Analysis Results. Each number represents the number of SNP sets called significant at the nominal α = 0:01 level by both the method along the top and the side of the table. Diagonal elements represent the number of SNP sets called significant by each individual method.

Table S8: Pre-term Birth Data Analysis Results. Each number represents the number of SNP sets called significant at the nominal α = 0:05 level by both the method along the top and the side of the table. Diagonal elements represent the number of SNP sets called significant by each individual method.

gepi21715-sup-0003-Suppmat.pdf104Ksupporting Information

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