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

addsamptreeTo determine whether the sampled tree will be accepted
AML43SNA input for primary tumor and relapse genome of leukemia...
canopy.BICTo get BIC as a model selection criterion
canopy.clusterEM algorithm for multivariate clustering of SNAs
canopy.cluster.EstepE-step of EM algorithm for multivariate clustering of SNAs
canopy.cluster.MstepM-step of EM algorithm for multivariate clustering of SNAs
canopy.outputTo generate a posterior tree
canopy.plottreeTo plot tree inferred by Canopy
canopy.postPosterior evaluation of MCMC sampled trees
canopy.sampleMCMC sampling in tree space
canopy.sample.clusterMCMC sampling in tree space with pre-clustering of SNAs
canopy.sample.cluster.nocnaMCMC sampling in tree space with pre-clustering of SNAs
canopy.sample.nocnaMCMC sampling in tree space
getclonalcompositionTo get clonal composition
getCMCmTo get major and minor copy per clone
getCZTo get CNA genotyping matrix CZ
getlikelihoodTo get likelihood of the tree
getlikelihood.snaTo get SNA likelihood of the tree
getQTo get SNA-CNA genotyping matrix
getVAFTo get variant allele frequency (VAF)
getZTo get SNA genotyping matrix Z
initialcnaTo initialize positions of CNAs
initialcnacopyTo initialize major and minor copies of CNAs
initialPTo initialize clonal frequency matrix
initialsnaTo initialize positions of SNAs
MDA231Dataset for project MDA231
MDA231_sampchainList of pre-sampled trees
MDA231_treeMost likely tree from project MDA231
sampcnaTo sample CNA positions
sampcnacopyTo sample major and minor copies of CNAs
sampPTo sample clonal frequency
sampsnaTo sample SNA positions
sampsna.clusterTo sample positions of SNA clusters
sortcnaTo sort identified overlapping CNAs.
toyToy dataset for Canopy
toy2Toy dataset 2 for Canopy
toy3Toy dataset 3 for Canopy
Canopy documentation built on Dec. 23, 2017, 5:09 p.m.