Accessing Intra-Tumor Heterogeneity and Tracking Longitudinal and Spatial Clonal Evolutionary History by Next-Generation Sequencing

Documentation for package ‘Canopy’ version 1.3.0

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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