Skip to main content

Table 3 H0-simulation: inflation factor and false-positive rates

From: Novel genetic matching methods for handling population stratification in genome-wide association studies

Test Units Validation N λ σ λ f p \({\sigma _{f_{p}}}\)
CAT AT 1845 1.990 0.013 0.167 0.001
CAT RSU All 1845 1.900 0.013 0.163 0.002
CAT RSU Pairs Cluster 1322 (661p) 0.853 0.008 0.044 0.001
CAT RSU Pairs Vicinity 1254 (627p) 0.846 0.007 0.044 0.001
CAT RSU Groups Cluster 1845 (661g) 0.921 0.006 0.047 0.001
CAT RSU Groups Vicinity 1845 (627g) 0.921 0.009 0.046 0.001
CAT RSU Clusters 1845 (14c) 0.918 0.006 0.046 0.001
MCAT(2) RSU Pairs Cluster 1322 (661p) 0.832 0.008 0.044 0.001
MCAT(2) RSU Pairs Vicinity 1254 (627p) 0.828 0.010 0.043 0.001
MCAT(2) RSU Groups Cluster 1845 (661g) 1.005 0.011 0.050 0.001
MCAT(2) RSU Groups Vicinity 1845 (627g) 1.001 0.011 0.050 0.001
MCAT(2) RSU Clusters 1845 (14c) 1.004 0.009 0.050 0.001
MCAT(1) AT Pairs Cluster 1322 (661p) 1.007 0.009 0.050 0.001
MCAT(1) AT Pairs Vicinity 1254 (627p) 1.007 0.011 0.050 0.001
MCAT(1) AT Groups Cluster 1845 (627g) 1.007 0.012 0.051 0.001
MCAT(1) AT Groups Vicinity 1845 (627g) 1.008 0.010 0.050 0.001
MCAT(1) AT Clusters 1845 (14c) 1.000 0.007 0.050 0.001
LRmds LRT 7 PCs 1845 1.201 0.019 0.078 0.001
LRmds LRT 14 PCs 1845 1.006 0.009 0.051 0.001
LRmds LRT 28 PCs 1845 1.017 0.009 0.052 0.001
  1. Given are means and standard errors of the inflation factor λ and false-positive rates f p from ten iterations of 1845 individuals and 44,900 SNPs. The nominal error level is α=0.05. The abbreviations in the second column are: AT asymptotic test, RSU resampling simulation within units (99,999 cycles), LRT likelihood ratio test. Column N shows the number of individuals included and in brackets the number of pairs p, groups g and clusters c.