Table 2 Simulation based performance comparison between the distance-type data and the count-type data (for the detection accuracy evaluation; W is the bin size)
From: A distance-type measure approach to the analysis of copy number variation in DNA sequencing data
p-value cutoff | Distance-type based proportion | Count-type based proportion, and test p-value for distance-type data vs. count-type data | ||
|---|---|---|---|---|
W = 25,000 bps | W = 10,000 bps | W = 5000 bps | ||
Region length L = 150,000 bps | ||||
 0.01 | 68.6% | 38.2%, < 10− 6 | 55.0%, 6 × 10− 6 | 57.0%, < 10− 6 |
 0.001 | 42.6% | < 0.1%, < 10− 6 | 28.1%, < 10− 6 | 32.9%, < 10− 6 |
 0.0001 | 24.7% | < 0.1%, < 10− 6 | 9.7%, < 10− 6 | 18.5%, < 10− 6 |
 0.00001 | 13.0% | < 0.1%, < 10− 6 | 3.1%, < 10− 6 | 8.9%, < 10− 6 |
 0.000001 | 6.3% | < 0.1%, < 10− 6 | 0.5%, < 10− 6 | 4.5%, 2 × 10− 5 |
 0.0000001 | 3.0% | < 0.1%, < 10− 6 | < 0.1%, < 10− 6 | 1.3%, < 10− 6 |
Region length L = 300,000 bps | ||||
 0.01 | 86.4% | 73.8%, > 0.99 | 78.1%, 0.929 | 78.8%, 7 × 10− 3 |
 0.001 | 70.3% | 46.6%, < 10− 6 | 58.8%, < 10− 6 | 62.1%, 2 × 10− 6 |
 0.0001 | 53.4% | 26.9%, < 10− 6 | 41.4%, < 10− 6 | 47.5%, 3 × 10− 5 |
 0.00001 | 39.9% | < 0.1%, < 10− 6 | 27.3%, < 10− 6 | 33.6%, < 10− 6 |
 0.000001 | 29.1% | < 0.1%, < 10− 6 | 19.1%, < 10− 6 | 24.2%, < 10− 6 |
 0.0000001 | 20.7% | < 0.1%, < 10− 6 | 10.1%, < 10− 6 | 17.6%, 3 × 10− 4 |
Region length L = 450,000 bps | ||||
 0.01 | 92.0% | 85.4%, > 0.99 | 87.7%, > 0.99 | 87.6%, 0.214 |
 0.001 | 81.0% | 69.3%, > 0.99 | 75.2%, 0.493 | 76.2%, 9 × 10− 3 |
 0.0001 | 69.1% | 49.2%, < 10− 6 | 60.9%, 1 × 10− 3 | 64.3%, 3 × 10− 3 |
 0.00001 | 57.5% | 35.3%, < 10− 6 | 49.1%, 1 × 10− 5 | 52.6%, 6 × 10− 4 |
 0.000001 | 48.0% | 14.7%, < 10− 6 | 38.0%, < 10− 6 | 43.4%, 5 × 10− 4 |
 0.0000001 | 38.9% | 5.5%, < 10− 6 | 28.6%, < 10− 6 | 36.1%, 0.041 |