Skip to main content

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.
Back to article page

BMC Genomic Data

ISSN: 2730-6844

Contact us