AML43                   SNA input for primary tumor and relapse genome
                        of leukemia patient from Ding et al. Nature
                        2012.
MDA231                  Dataset for project MDA231
MDA231_sampchain        List of pre-sampled trees
MDA231_tree             Most likely tree from project MDA231
addsamptree             To determine whether the sampled tree will be
                        accepted
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
getCMCm                 To get major and minor copy per clone
getCZ                   To get CNA genotyping matrix CZ
getQ                    To get SNA-CNA genotyping matrix
getVAF                  To get variant allele frequency (VAF)
getZ                    To get SNA genotyping matrix Z
getclonalcomposition    To get clonal composition
getlikelihood           To get likelihood of the tree
getlikelihood.sna       To get SNA likelihood of the tree
initialP                To initialize clonal frequency matrix
initialcna              To initialize positions of CNAs
initialcnacopy          To initialize major and minor copies of CNAs
initialsna              To initialize positions of SNAs
sampP                   To sample clonal frequency
sampcna                 To sample CNA positions
sampcnacopy             To sample major and minor copies of CNAs
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
