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Table 5 Empirical selection probability of significant SNP pairs by S LASSO and S SCAD under subsampling

From: Stability SCAD: a powerful approach to detect interactions in large-scale genomic study

 

Trait

  

Nanjing Study

Beijing Study

Pooled Study

SNP1(rs)

Gene1

SNP2(rs)

Gene2

a Π

bp

Π

p

Π

p

SLASSO

SSCAD

Marginal

SLASSO

SSCAD

Marginal

SLASSO

SSCAD

Marginal

rs7839119

PTK2

rs12544802

PTK2

0.724c*

0.702*

1.04 × 10-6

0.628*

0.940*

6.34 × 10-2

0.668*

0.801*

3.10 × 10-4

rs3781626

RAPSN

rs6018348

SRC

0.734*

0.680*

3.25 × 10-3

0.514*

0.654*

2.88 × 10-3

0.617*

0.824*

1.40 × 10-4

rs7839119

PTK2

rs4524871

MUSK

0.746*

0.734*

7.19 × 10-4

0.478

0.518*

4.98 × 10-2

0.600*

0.980*

5.02 × 10-4

rs2736100

TERT

rs40318

PIK3R1

0.586

0.830*

9.87 × 10-6

0.390

0.582*

2.22 × 10-2

0.696*

0.977*

2.51 × 10-6

  1. aΠ represents the empirical selection probability of SNP pairs under subsampling.
  2. bp stands for the trend test p-value for simple marginal logistic regression.
  3. cThe significant SNP pairs under stability selection are coded by (*) to indicate its selection probability being higher than the threshold value (implied by FDR < 0.1).
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BMC Bioinformatics

ISSN: 1471-2105

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