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Table 1 Number of positive genes and estimated FDR

From: Comparison of SNP-based and gene-based association studies in detecting rare variants using unrelated individuals

Trait

Method

α = 0.25

α = 0.5

α = 0.75

  

No. Pos

FDR

No. Pos

FDR

No. Pos

FDR

Q1

SNP

35.185

0.849

51.625

0.874

65.875

0.884

 

GL

31.790

0.791

47.935

0.837

65.100

0.869

 

G2

26.785

0.777

39.730

0.823

47.255

0.841

Q2

SNP

3.975

0.281

11.060

0.486

29.905

0.655

 

GL

4.175

0.297

12.350

0.503

29.315

0.662

 

G2

4.370

0.351

13.755

0.545

27.760

0.684

Q4

SNP

0.325

–

1.215

–

3.210

–

 

GL

0.365

–

1.120

–

3.370

–

 

G2

0.415

–

1.325

–

2.900

–

D

SNP

3.695

0.324

12.690

0.519

33.940

0.580

 

GL

5.225

0.261

17.355

0.374

37.050

0.476

 

GS

4.945

0.274

13.615

0.377

34.330

0.437

 

G2

5.575

0.284

19.160

0.416

33.880

0.467

  1. SNP, GL, G2, and GS are the SNP-based, gene-based linear, gene-based two-step, and gene-based similarity methods, respectively. α is the predefined value in the BH procedure. “No. POS” is the average number of positives over 200 replicates; and the FDR is the observed false discovery rate.
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BMC Proceedings

ISSN: 1753-6561

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