Varying parameters and their ranges for synthetic data simulation.

For each experiment, we varied one parameter and kept the others fixed. Note that varying the number of regions is equivalent to varying region size because the total number of loci is fixed. Unless otherwise specified, the fixed parameters are: missing proportion 0.8, region size 100, number of cells 100, proportion of cell-to-cell variability 0, number of epiclones 3, equal epiclone frequencies (1/3), number of loci 10,000, and number of regions different between clusters 1. For the cell-to-cell variability experiment (Fig 4c), we used 25 regions to have a larger number of loci that differed between clusters. For the number of epiclones experiment (Fig 4d) and the epiclone frequency experiment (Fig 4e), we used 500 cells to allow for enough cells to be represented in each case. For the number of loci experiment (Fig 4f), we also varied the number of regions to keep the differences among clusters fixed (e.g., 50 regions for 5,000 loci, 5,000 regions for 500,000 loci).