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Table 1 Summary of p-values, estimated power and size of tagSNP sets over 100 replicates

From: A comparison of five methods for selecting tagging single-nucleotide polymorphisms

   D2 Region D4 Region
Method Sample Median p-valuea [1st, 3rd quartile] Estimated powerb (SE) Mean # tagSNPs (SD) Median p-valuea [1st, 3rd quartile] Estimated powerb (SE) Mean # tagSNPs (SD)
Cousin cases 0.034 [0.0002, 0.0173] 0.88 (0.033) 16.5 (0.6) 0.050 [0.0131, 0.1043] 0.49 (0.051) 20.2 (0.9)
  controls 0.021 [0.0002, 0.0173] 0.88 (0.033) 16.6 (0.5) 0.041 [0.0134, 0.1113] 0.53 (0.050) 20.7 (0.8)
  mixture 0.033 [0.0002, 0.0176] 0.87 (0.034) 16.5 (0.6) 0.040 [0.0125, 0.1124] 0.55 (0.050) 20.7 (0.7)
Chapman-allelic cases 0.002 [0.0002, 0.0176] 0.88 (0.033) 16.9 (0.3) 0.050 [0.0129, 0.2307] 0.50 (0.050) 20.0 (1.0)
  controls 0.002 [0.0002, 0.0176] 0.88 (0.033) 16.8 (0.4) 0.047 [0.0136, 0.1792] 0.50 (0.050) 20.8 (0.8)
  mixture 0.002 [0.0002, 0.0176] 0.88 (0.033) 16.9 (0.4) 0.041 [0.0135, 0.1261] 0.52 (0.050) 20.5 (0.9)
Stram cases 0.013 [0.0032, 0.0505] 0.73 (0.044) 7.8 (0.6) 0.042 [0.0101, 0.2754] 0.53 (0.050) 8.1 (1.0)
  controls 0.003 [9 × 10-5, 0.0348] 0.76 (0.043) 7.9 (0.7) 0.069 [0.0066, 0.2745] 0.44 (0.050) 8.0 (1.1)
  mixture 0.008 [4 × 10-4, 0.0769] 0.70 (0.046) 7.7 (0.6) 0.075 [0.0133, 0.2368] 0.46 (0.050) 7.9 (1.0)
Zhaic (Stram) cases 0.039 [0.0126, 0.146] 0.59 (0.049)   0.099 [0.0141, 0.2564] 0.44 (0.050)  
  controls 0.039 [0.0088, 0.1642] 0.59 (0.049)   0.080 [0.0132, 0.2562] 0.46 (0.050)  
  mixture 0.037 [0.0112, 0.1538] 0.58 (0.049)   0.059 [0.0124, 0.2565] 0.50 (0.050)  
Chapman-haplotypic cases 0.022 [0.0052, 0.1553] 0.64 (0.048) 6.9 (0.4) 0.150 [0.0143, 0.5386] 0.37 (0.048) 7.6 (0.6)
  controls 0.011 [0.0006, 0.1126] 0.68 (0.047) 6.8 (0.4) 0.105 [0.0197, 0.3639] 0.37 (0.048) 7.5 (0.6)
  mixture 0.016 [0.0014, 0.0970] 0.66 (0.047) 6.9 (0.5) 0.115 [0.0152, 0.4258] 0.41 (0.049) 7.5 (0.6)
Zhaid (Chapman haplotypic) cases 0.041 [0.0116, 0.1805] 0.61 (0.049)   0.048 [0.0103, 0.2322] 0.50 (0.050)  
  controls 0.022 [0.0060, 0.1126] 0.67 (0.047)   0.055 [0.0108, 0.2196] 0.49 (0.050)  
  mixture 0.037 [0.0086, 0.1620] 0.62 (0.049)   0.059 [0.0107, 0.2192] 0.48 (0.050)  
  1. aThe median of the Bonferroni-corrected p-values from 100 replicates.
  2. bThe proportion of replicates with Bonferroni-corrected p-value < 0.05.
  3. cThe number of tagSNPs chosen for Zhai is set to be the same as Stram for each sample within replicate.
  4. dThe number of tagSNPs chosen for Zhai is set to be the same as Chapman-haplotypic for each sample within replicate.