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Table 3 Comparisons between the proposed method and Park's method.

From: Shrunken methodology to genome-wide SNPs selection and construction of SNPs networks

  

The Proposed Method

Park's Method

Chromosome

Number of SNPs

Accuracy

Δ

Number of SNPs

Accuracy

Δ

Number of SNPs

1

29226

0.5926

0.893

21

0.5667

0.876

88

2

30298

0.6019

0.919

20

0.5722

0.965

87

3

25648

0.6056

0.880

26

0.5611

0.860

132

4

22315

0.6204

0.918

11

0.5945

1.024

42

5

22746

0.5796

0.926

22

0.5611

0.900

82

6

24334

0.6093

1.003

3

0.5204

0.944

49

7

19740

0.5797

0.901

7

0.5685

0.980

39

8

21384

0.5834

0.931

6

0.5741

0.979

35

9

18122

0.5426

0.932

7

0.5148

0.908

61

10

18525

0.6074

0.930

9

0.5593

0.999

47

11

18074

0.6352

0.964

7

0.5944

0.942

52

12

18186

0.6074

0.893

17

0.5667

0.975

31

13

13077

0.5870

0.906

9

0.5053

0.919

23

14

11728

0.5574

0.901

8

0.5259

0.962

26

15

10813

0.6037

0.905

8

0.5556

0.917

40

16

10892

0.5778

0.936

8

0.5611

0.946

37

17

10730

0.5815

0.919

4

0.5037

0.961

31

18

11677

0.5704

0.921

5

0.5071

0.956

27

19

7749

0.6037

0.887

7

0.5463

0.950

13

20

9647

0.6111

0.864

12

0.5907

0.951

33

21

6070

0.5833

0.875

8

0.4945

0.911

8

22

6459

0.6056

0.901

5

0.5444

0.924

23

Average

0.5930

0.914

10

0.5495

0.943

46

  1. Illustration of the classification accuracies of all chromosomes of Parkinson disease genome-wide data set after a 10-fold cross validation and a detailed comparison between our proposed method and Park's method when filter out those SNPs whose missing percentage is >1%. The second column indicates the number of SNPs in each chromosome after filtering. Accuracy is the average accuracy after a 10-fold cross validation, Δ value and No of SNPs are obtained when the corresponding average accuracy is reached.