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Table 4 Precision and recall values of PSE-HMM are compared to m-HMM, Pindel, CNV-seq, and Delly

From: PSE-HMM: genome-wide CNV detection from NGS data using an HMM with Position-Specific Emission probabilities

  Coverage
10×
Precision mean/std Recall mean/std F-measure Precision mean/std Recall mean/std F-measure Precision mean/std Recall mean/std F-measure
Duplications PSE-HMM 0.91/0.03 0.79/0.02 0.85 0.92/0.02 0.95/0.01 0.93 0.88/0.01 0.97/0.02 0.92
m-HMM 0.95/0.01 0.21/0.02 0.35 1.00/0.02 0.64/0.02 0.78 1.00/0.01 0.71/0.01 0.83
Pindel 1.00/0.00 0.11/0.04 0.20 1.00/0.00 0.67/0.03 0.80 1.00/0.01 0.81/0.03 0.90
CNV-seq 0.55/0.03 0.41/0.03 0.47 0.98/0.00 0.54/0.03 0.70 0.99/0.00 0.57/0.03 0.72
Delly 1.00/0.00 0.80/0.05 0.89 1.00/0.00 0.99/0.05 0.99 1.00/0.00 1.00/0.00 1.00
Deletions PSE-HMM (heterozygous) 0.43/0.03 0.37/0.03 0.40 0.54/0.04 0.97/0.01 0.69 0.60/0.02 1.00/0.02 0.75
PSE-HMM (homozygous) 0.20/0.03 0.92/0.05 0.33 0.73/0.03 0.97/0.02 0.83 0.81/0.02 0.93/0.03 0.87
PSE-HMM (hetero + homo)a 0.31/0.03 0.86/0.02 0.46 0.63/0.02 0.99/0.01 0.77 0.72/0.03 1.00/0.03 0.84
m-HMM (heterozygous) 0.67/0.02 0.16/0.04 0.25 0.93/0.03 0.88/0.03 0.91 0.93/0.03 0.92/0.02 0.93
m-HMM (homozygous) 0.95/0.02 0.65/0.02 0.77 0.99/0.02 0.62/0.02 0.77 0.99/0.01 0.62/0.03 0.77
m-HMM (hetero + homo)a 0.93/0.02 0.43/0.03 0.59 0.99/0.01 0.78/0.02 0.87 0.99/0.02 0.80/0.03 0.88
Pindel 0.93/0.15 0.02/0.01 0.04 0.91/0.03 0.36/0.02 0.52 0.87/0.06 0.45/0.05 0.59
CNV-seq 0.72/0.05 0.75/0.02 0.73 0.98/0.00 0.91/0.01 0.94 0.98/0.00 0.95/0.01 0.96
Delly 0.98/0.00 0.32/0.04 0.48 0.99/0.00 0.48/0.03 0.65 0.99/0.00 0.49/0.04 0.66
Diploid PSE-HMM 0.96/0.00 0.79/0.01 0.87 0.99/0.00 0.93/0.00 0.96 1.00/0.00 0.96/0.00 0.98
m-HMM 0.87/0.01 1.00/0.01 0.93 0.94/0.00 1.00/0.00 0.97 0.95/0.00 1.00/0.00 0.97
Pindel 0.82/0.01 1.00/0.00 0.90 0.90/0.01 1.00/0.00 0.95 0.93/0.01 1.00/0.00 0.96
CNV-seq 0.91/0.00 0.93/0.00 0.92 0.94/0.00 1.00/0.00 0.97 0.95/0.00 1.00/0.00 0.97
Delly 0.91/0.01 1.00/0.00 0.95 0.94/0.01 1.00/0.00 0.97 0.94/0.01 1.00/0.00 0.97
  1. For each method, the average and standard deviation of the precision (recall) values over five different runs of the whole simulation study are given in each cell. For each state i.e. tandem duplication, deletion and diploid, evaluations are done for three different coverage values i.e. 1×, 5×, and 10×. The implanted CNVs are of length 1 kb, 1.5 kb, 2 kb, 2.5 kb, …, 4.5 kb, and 5 kb
  2. a hetero + homo stands for copy loss