| addsamptree | To determine whether the sampled tree will be accepted |
| AML43 | SNA input for primary tumor and relapse genome of leukemia patient from Ding et al. Nature 2012. |
| canopy.BIC | To get BIC as a model selection criterion |
| canopy.cluster | EM algorithm for multivariate clustering of SNAs |
| canopy.cluster.Estep | E-step of EM algorithm for multivariate clustering of SNAs |
| canopy.cluster.Mstep | M-step of EM algorithm for multivariate clustering of SNAs |
| canopy.output | To generate a posterior tree |
| canopy.plottree | To plot tree inferred by Canopy |
| canopy.post | Posterior evaluation of MCMC sampled trees |
| canopy.sample | MCMC sampling in tree space |
| canopy.sample.cluster | MCMC sampling in tree space with pre-clustering of SNAs |
| canopy.sample.cluster.nocna | MCMC sampling in tree space with pre-clustering of SNAs |
| canopy.sample.nocna | MCMC sampling in tree space |
| getclonalcomposition | To get clonal composition |
| getCMCm | To get major and minor copy per clone |
| getCZ | To get CNA genotyping matrix CZ |
| getlikelihood | To get likelihood of the tree |
| getlikelihood.sna | To get SNA likelihood of the tree |
| getQ | To get SNA-CNA genotyping matrix |
| getVAF | To get variant allele frequency (VAF) |
| getZ | To get SNA genotyping matrix Z |
| initialcna | To initialize positions of CNAs |
| initialcnacopy | To initialize major and minor copies of CNAs |
| initialP | To initialize clonal frequency matrix |
| initialsna | To initialize positions of SNAs |
| MDA231 | Dataset for project MDA231 |
| MDA231_sampchain | List of pre-sampled trees |
| MDA231_tree | Most likely tree from project MDA231 |
| sampcna | To sample CNA positions |
| sampcnacopy | To sample major and minor copies of CNAs |
| sampP | To sample clonal frequency |
| sampsna | To sample SNA positions |
| sampsna.cluster | To sample positions of SNA clusters |
| sortcna | To sort identified overlapping CNAs. |
| toy | Toy dataset for Canopy |
| toy2 | Toy dataset 2 for Canopy |
| toy3 | Toy dataset 3 for Canopy |