Canopy: Accessing Intra-Tumor Heterogeneity and Tracking Longitudinal and Spatial Clonal Evolutionary History by Next-Generation Sequencing
Version 1.2.0

A statistical framework and computational procedure for identifying the sub-populations within a tumor, determining the mutation profiles of each subpopulation, and inferring the tumor's phylogenetic history. The input are variant allele frequencies (VAFs) of somatic single nucleotide alterations (SNAs) along with allele-specific coverage ratios between the tumor and matched normal sample for somatic copy number alterations (CNAs). These quantities can be directly taken from the output of existing software. Canopy provides a general mathematical framework for pooling data across samples and sites to infer the underlying parameters. For SNAs that fall within CNA regions, Canopy infers their temporal ordering and resolves their phase. When there are multiple evolutionary configurations consistent with the data, Canopy outputs all configurations along with their confidence assessment.

AuthorYuchao Jiang, Nancy R. Zhang
Date of publication2017-04-08 20:30:16 UTC
MaintainerYuchao Jiang <yuchaoj@wharton.upenn.edu>
LicenseGPL-2
Version1.2.0
URL https://github.com/yuchaojiang/Canopy
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("Canopy")

Popular man pages

AML43: SNA input for primary tumor and relapse genome of leukemia...
canopy.cluster: EM algorithm for multivariate clustering of SNAs
canopy.cluster.Mstep: M-step of EM algorithm for multivariate clustering of SNAs
getCZ: To get CNA genotyping matrix CZ
getlikelihood.sna: To get SNA likelihood of the tree
initialcna: To initialize positions of CNAs
toy: Toy dataset for Canopy
See all...

All man pages Function index File listing

Man pages

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

Functions

Files

inst
inst/doc
inst/doc/Canopy_vignettes.Rnw
inst/doc/Canopy_vignettes.pdf
inst/doc/Canopy_vignettes.R
NAMESPACE
NEWS
data
data/toy3.rda
data/toy2.rda
data/MDA231_tree.rda
data/MDA231_sampchain.rda
data/MDA231.rda
data/AML43.rda
data/toy.rda
R
R/addsamptree.R
R/initialsna.R
R/canopy.sample.cluster.nocna.R
R/getVAF.R
R/canopy.sample.cluster.R
R/canopy.cluster.Estep.R
R/sampsna.cluster.R
R/sampcnacopy.R
R/canopy.sample.nocna.R
R/getlikelihood.R
R/getlikelihood.sna.R
R/sampcna.R
R/canopy.sample.R
R/initialcna.R
R/getZ.R
R/getCZ.R
R/sortcna.R
R/canopy.output.R
R/canopy.cluster.Mstep.R
R/canopy.post.R
R/canopy.BIC.R
R/canopy.cluster.R
R/initialcnacopy.R
R/sampsna.R
R/sampP.R
R/getQ.R
R/getclonalcomposition.R
R/initialP.R
R/canopy.plottree.R
R/getCMCm.R
vignettes
vignettes/Canopy_vignettes.Rnw
MD5
build
build/vignette.rds
DESCRIPTION
man
man/canopy.plottree.Rd
man/MDA231.Rd
man/canopy.BIC.Rd
man/sampsna.Rd
man/addsamptree.Rd
man/getZ.Rd
man/getQ.Rd
man/toy2.Rd
man/sampcna.Rd
man/canopy.sample.cluster.nocna.Rd
man/toy.Rd
man/getCZ.Rd
man/initialsna.Rd
man/MDA231_tree.Rd
man/canopy.cluster.Estep.Rd
man/canopy.cluster.Mstep.Rd
man/sampP.Rd
man/sampcnacopy.Rd
man/getlikelihood.sna.Rd
man/MDA231_sampchain.Rd
man/getVAF.Rd
man/canopy.post.Rd
man/getlikelihood.Rd
man/canopy.sample.cluster.Rd
man/initialP.Rd
man/initialcna.Rd
man/AML43.Rd
man/canopy.sample.Rd
man/toy3.Rd
man/canopy.sample.nocna.Rd
man/canopy.output.Rd
man/initialcnacopy.Rd
man/canopy.cluster.Rd
man/getCMCm.Rd
man/sortcna.Rd
man/sampsna.cluster.Rd
man/getclonalcomposition.Rd
Canopy documentation built on May 19, 2017, 8:53 p.m.

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