Skip to main content

Table 2 Computational performance

From: Copynumber: Efficient algorithms for single- and multi-track copy number segmentation

Method

R package

Agilent 244K

Illumina 1.1M

  

Raw data

Outliers removed

Raw data

Outliers removed

PCF

copynumber

4 (0.2)

4 (0.2)

23 (0.7)

22 (0.4)

Fused Lasso

cghFLasso

5 (0.2)

5 (0.2)

97 (0.7)

99 (3.3)

CBS

DNAcopy

15 (4.7)

35 (4.1)

71 (12.9)

219 (12.8)

  1. The average computation time (in seconds) per sample is shown for copynumber (PCF), DNAcopy v1.30.0 (CBS) and cghFLasso v0.2-1 (Fused Lasso) on the MicMa 244 K data set (49 samples) and on the logR values from an Illumina 1.1 M SNP array data set (6 samples). The IQR over samples is given in parenthesis. The methods were applied to both raw data and data with outliers removed using the Winsorization method. All tests were performed on a PC with a 2.93GHz Intel i7 CPU with 8 Gb of memory running Windows 7 and R 2.15.1 (64-bit).