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Table 2 Computational performance

From: DBS: a fast and informative segmentation algorithm for DNA copy number analysis

Method

Time (s)

Trend Line

Test 1

(26 K, 1 Chr.)

Test 2

(160 K, 1 Chr.)

Affymetrix SNP 6.0 (868 K, 22 Chr.)

Slope

R2

In BACOM

0.592

18.769

34.818

1.999

0.988

 CBS

1.442

6.249

80.551

0.984

0.963

 PCF

0.393

2.638

10.256

0.968

0.979

 DBS

0.093

0.524

2.167

0.968

0.986

  1. The computation time (in seconds) is shown for DNAcopy v1.52.0 (CBS), copynumber v1.18 (PCF), in BACOM, and DBS (ToolSeg) on the 26 K / 160 K simulation data set (10 samples) and on the values from an Affymetrix SNP 6.0 Array data set (10 samples). The slope of linear trend lines represents the computational complexity of each algorithm, which are shown in Fig. 5. All tests were performed on a PC with a 2.5GHz Intel i5 CPU with 8 GB of memory running Windows 10 and Java 8 (64-bit)
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BMC Bioinformatics

ISSN: 1471-2105

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