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Table 1 Detection accuracy and computation time of four methods on simulated normal samples

From: Reconstructing DNA copy number by joint segmentation of multiple sequences

CNV size CNV type   PennCNV   CBS   Fused Lasso   Group Fused Lasso
    TPR FDR   TPR FDR   TPR FDR   TPR FDR
5 Deletion   83.80 4.92   78.20 0.68   63.93 1.74   64.27 1.83
  Duplication   58.53 4.67   11.67 10.26   20.00 37.76   39.87 14.33
10 Deletion   95.03 1.45   88.37 0.56   88.50 0.60   88.87 0.56
  Duplication   93.43 0.78   56.50 4.40   83.90 12.60   91.60 3.85
20 Deletion   94.63 0.58   90.50 0.39   90.80 0.47   90.83 0.47
  Duplication   96.13 0.92   86.22 3.58   92.77 4.95   94.98 2.13
30 Deletion   94.57 0.28   93.30 0.29   89.38 0.52   89.77 0.53
  Duplication   96.09 0.05   90.77 1.61   94.32 1.78   94.98 1.29
40 Deletion   97.83 0.59   97.58 0.09   97.28 0.19   97.28 0.19
  Duplication   94.61 0.46   92.77 0.98   93.94 1.15   94.63 0.75
50 Deletion   94.33 0.07   92.76 0.04   90.47 0.11   90.48 0.11
  Duplication   94.50 0.09   93.81 0.74   93.11 0.79   93.64 0.49
 Overall Deletion   95.02 0.55   93.06 0.19   91.08 0.33   91.19 0.34
 Overall Duplication   93.82 0.44   86.92 1.55   90.56 2.85   92.46 1.38
 Overall   94.42 0.49   89.99 0.85   90.82 1.60   91.83 0.87
Time (sec.)   0.48 (0.01)   0.78 (0.69)   0.22 (0.13)   0.28 (0.05)
  1. TPR and FDR are measured as the percentage of related SNPs. Overall accuracy is calculated by pooling all sequences with a given type of CNV. Also reported are the average and standard deviation of the number of seconds required for the analysis of one sequence.