Table 1 Factors considered and their levels or possible values, together with acronyms used through the text
Factor | Description | Values |
|---|---|---|
Model | Evolutionary model of cancer progression | exp, Bozic, McF_4, McF_6 |
sh | Penalization of deviations from monotonicity | 0, Inf (for ∞) |
True graph | The true graph: the structure that encodes the order restrictions. All possible combinations of Number of nodes and Conjunction | 11-A, 11-B, 9-A, 9-B, 7-A, 7-B |
Number of nodes (NumNodes) | Number of genes or alterations | 11, 9, 7 |
Conjunction | Whether or not the graph has conjunctions | Yes, No |
Sample size (S.Size) | Number of samples used for reconstructing the graph | 100, 200, 1000 |
Sampling time (S.Time) | When the sample is taken | Last, unif (for uniform) |
Sampling type (S.Type) | How tissue is collected | singleC (for single cell), wholeT_0.5 (whole tumor, detection threshold=0.5), wholeT_0.01 (whole tumor, detection threshold=0.1) |
Filtering | Method for selecting drivers, or filtering passengers, when the true drivers are not known | S1, S5, J1, J5 (for frequency of Single event and Joint frequency of events, with thresholds 1% and 5% respectively) |
Method | Method for inferring the order restrictions | CBN, CBN-A, DiP, DiP-A, OT, OT-A |