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Table 1 Computational time required by MDR, RF and 2LOmb to analyse small-scaled simulated data sets with different numbers of available SNPs, different numbers of causative SNPs and different ratios of case samples from two affected groups

From: An omnibus permutation test on ensembles of two-locus analyses can detect pure epistasis and genetic heterogeneity in genome-wide association studies

Number of

Ratio

Computational time (sec)

causative

of case

MDR

RF

2LOmb

SNPs

samples

20 SNPs

20 SNPs

1,000 SNPs

20 SNPs

1,000 SNPs

2&2

1:3

6,505

2

539

5

24

 

1:1

6,434

2

529

6

23

3&3

1:3

6,573

2

529

13

32

 

1:1

6,611

2

531

14

32

4&4

1:3

6,372

2

534

32

45

 

1:1

6,528

2

538

27

46

2&3

1:3

6,637

2

529

12

32

 

1:1

6,644

3

527

10

30

 

3:1

6,776

2

528

10

28

2&4

1:3

6,513

2

525

16

35

 

1:1

6,637

2

528

16

35

 

3:1

6,599

2

528

18

34

3&4

1:3

6,369

2

526

22

38

 

1:1

6,410

2

530

25

45

 

3:1

6,435

2

528

22

38

  1. The simulation is carried out on a computer server. The computer server is equipped with a Xeon 2.66 GHz quad-core processor and 4GB of main memory. A CentOS 5.5 operating system is installed on the computer server. The computational time is collected from the processing of multiple independent data sets for each simulation setting. The displayed time is the maximum time required by each algorithm to analyse one data set.
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