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

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.

Author
Yuchao Jiang, Nancy R. Zhang
Date of publication
2016-09-02 22:26:50
Maintainer
Yuchao Jiang <yuchaoj@wharton.upenn.edu>
License
GPL-2
Version
1.1.1
URLs

View on CRAN

Man pages

addsamptree
To determine whether the sampled tree will be accepted
canopy.BIC
To get BIC as a model selection criterion
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
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
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
plotpostlikelihood
To plot posterior likelihood
sampcna
To sample CNA positions
sampcnacopy
To sample major and minor copies of CNAs
sampP
To sample clonal frequency
sampsna
To sample SNA positions
sortcna
To sort identified overlapping CNAs.
toy
Toy dataset for Canopy
toy2
Toy dataset 2 for Canopy

Files in this package

Canopy
Canopy/inst
Canopy/inst/doc
Canopy/inst/doc/Canopy_vignettes.Rnw
Canopy/inst/doc/Canopy_vignettes.pdf
Canopy/inst/doc/Canopy_vignettes.R
Canopy/NAMESPACE
Canopy/NEWS
Canopy/data
Canopy/data/toy2.rda
Canopy/data/MDA231_tree.rda
Canopy/data/MDA231_sampchain.rda
Canopy/data/MDA231.rda
Canopy/data/toy.rda
Canopy/R
Canopy/R/addsamptree.R
Canopy/R/initialsna.R
Canopy/R/getVAF.R
Canopy/R/sampcnacopy.R
Canopy/R/getlikelihood.R
Canopy/R/plotpostlikelihood.R
Canopy/R/sampcna.R
Canopy/R/canopy.sample.R
Canopy/R/initialcna.R
Canopy/R/getZ.R
Canopy/R/getCZ.R
Canopy/R/sortcna.R
Canopy/R/canopy.output.R
Canopy/R/canopy.post.R
Canopy/R/canopy.BIC.R
Canopy/R/initialcnacopy.R
Canopy/R/sampsna.R
Canopy/R/sampP.R
Canopy/R/getQ.R
Canopy/R/getclonalcomposition.R
Canopy/R/initialP.R
Canopy/R/canopy.plottree.R
Canopy/R/getCMCm.R
Canopy/vignettes
Canopy/vignettes/Canopy_vignettes.Rnw
Canopy/MD5
Canopy/build
Canopy/build/vignette.rds
Canopy/DESCRIPTION
Canopy/man
Canopy/man/canopy.plottree.Rd
Canopy/man/MDA231.Rd
Canopy/man/canopy.BIC.Rd
Canopy/man/sampsna.Rd
Canopy/man/addsamptree.Rd
Canopy/man/getZ.Rd
Canopy/man/getQ.Rd
Canopy/man/toy2.Rd
Canopy/man/sampcna.Rd
Canopy/man/toy.Rd
Canopy/man/getCZ.Rd
Canopy/man/initialsna.Rd
Canopy/man/MDA231_tree.Rd
Canopy/man/plotpostlikelihood.Rd
Canopy/man/sampP.Rd
Canopy/man/sampcnacopy.Rd
Canopy/man/MDA231_sampchain.Rd
Canopy/man/getVAF.Rd
Canopy/man/canopy.post.Rd
Canopy/man/getlikelihood.Rd
Canopy/man/initialP.Rd
Canopy/man/initialcna.Rd
Canopy/man/canopy.sample.Rd
Canopy/man/canopy.output.Rd
Canopy/man/initialcnacopy.Rd
Canopy/man/getCMCm.Rd
Canopy/man/sortcna.Rd
Canopy/man/getclonalcomposition.Rd