Man pages for SunPathLab/Butte
BoUnds of Time Till Expansion, inferring the SCNA arrival time in the somatic evolution toward the most recent common ancestor of tumor sample(s).
| bootstrapButte | Bootstrap for the CI of timing estimates |
| Butte | Calculate timing of SCNA |
| cnmutData | Generate the SCNA SSNV input for running butte |
| cnmutHistory | generate history matrix in relating SCNA to SSNVs |
| dot-estimateQ | EM algorithm to calculate q |
| dot-lpbounds | Use linear programming to solve the bounds of TK or T0 |
| mergeCNA | Merge the CNA by jumping (neglecting) small segments |
| scnaInput | Reading and sorting scnaFile |
| scnaTiming | estimate the initiation and arrival time for each SCNA... |
| ssnvInput | Reading and sorting ssnvFile |
| vafEst | Return the allele frequencies of SSNVs for each allele state |
