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Table 1 Summary of validation of the three methods

From: Application of Bayesian regression with singular value decomposition method in association studies for sequence data

 

Empirical outcome

 

Single-SNP association

PR method

BRSVD method

Actual outcome

E′ (= 50)

IE′ (= 24,437)

 

E′ (= 16)

IE′ (= 24,471)

 

E′ (= 45)

IE′ (= 24,442)

 

E (= 39)

TP = 2

FN = 37

Sen = 0.051

TP = 3

FN = 36

Sen = 0.077

TP = 9

FN = 30

Sen = 0.231

IE (= 24,448)

FP = 48

TN = 24,400

Spe = 0.998

FP = 13

TN = 24,435

Spe = 0.9995

FP = 36

TN = 24,412

Spe = 0.9985

 

PPV = 0.04

NPV = 0.9984

 

PPV = 0.187

NPV = 0.9985

 

PPV = 0.2

NPV = 0.9988

 
  1. Empirical analysis results for the three methods. E is the number of SNPs that are truly effective, IE is the number of SNPs that are ineffective). E` is the number of SNPs that are empirically effective, IE is the number of SNPs that are ineffective); TP, true positive; FP, false positive; FN, false negative; TN, true negative; PPV, positive predictive value; NPV, negative predictive value; Sen, sensitivity; Spe, specificity.
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BMC Proceedings

ISSN: 1753-6561

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