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

addsamptree | To determine whether the sampled tree will be accepted |

AML43 | SNA input for primary tumor and relapse genome of leukemia... |

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 |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.