addsamptree | To determine whether the sampled tree will be accepted |
canopy.BIC | To get BIC as a model selection criterion |
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 |
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 |
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 |
plotpostlikelihood | To plot posterior likelihood |
sampcna | To sample CNA positions |
sampcnacopy | To sample major and minor copies of CNAs |
sampP | To sample clonal frequency |
sampsna | To sample SNA positions |
sortcna | To sort identified overlapping CNAs. |
toy | Toy dataset for Canopy |
toy2 | Toy dataset 2 for Canopy |