Clique-Based Clustering of Correlated SNPs in a Gene Can Improve Performance of Gene-Based Multi-Bin Linear Combination Test

Table 2

Mean and standard deviation over 1000 genes of agreement measure and for two clustering methods (LDSelect and CLQ) and number of genes with identical clustering.

Allele frequency cut						Cases of perfect agreement
		Mean	SD	Mean	SD
.05	.3	.676	0.203	.325	0.342	180
	.4	.769	0.191	.510	0.336	283
	.5	.847	0.168	.665	0.303	388
	.6	.909	0.123	.781	0.242	483
	.7	.936	0.101	.832	0.210	541
	.8	.959	0.086	.884	0.178	648
	.9	.974	0.069	.918	0.156	736
.01	.3	.689	0.196	.395	0.376	155
	.4	.789	0.177	.559	0.379	254
	.5	.863	0.151	.687	0.338	361
	.6	.923	0.105	.794	0.267	468
	.7	.948	0.084	.843	0.230	536
	.8	.968	0.068	.892	0.201	644
	.9	.981	0.053	.922	0.172	744