Table 3 Description of the measures used in the DeviCNV scoring system
Abbreviation | Description | Calculation method | Default parameter setting |
|---|---|---|---|
ProbeCntInRegion | How many signals support the CNV candidate? | Counting read depth ratio signals for a CNV candidate | 1 point for ≥2 |
AverageOfReadDepthRatios | How strong is the signal supporting the CNV candidate? | Calculating an average log2-transformed median predicted probe-level read depth ratio values for a CNV candidate | If deletion, 1 point for < log2(0.6); If duplication, 1 point for > log2(1.4) |
STDOfReadDepthRatios | How stable are the signals supporting the CNV candidate? | Calculating a standard deviation for the log2-transformed median predicted probe-level read depth ratio values for a CNV candidate | 1 point for < 0.4 |
AverageOfCIs | How small are the confidence intervals for the signals supporting the CNV candidate? | Calculating average log2-transformed 95% confidence interval lengths for predicted probe-level read-depth ratios for a CNV candidate | 1 point for < 0.4 |
AverageOfR2vals | How reliable is the model that generated the signals that support the CNV candidate? | Calculating average mean R-squared values per probe for a CNV candidate, with the average R-squared value per probe referring to an average of the R-squared values of N models for one probe | 1 point for ≥0.85 |