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.

AuthorYuchao Jiang, Nancy R. Zhang
Date of publication2016-09-02 22:26:50
MaintainerYuchao Jiang <yuchaoj@wharton.upenn.edu>
LicenseGPL-2
Version1.1.1
https://github.com/yuchaojiang/Canopy

View on CRAN

Functions

addsamptree Man page
canopy.BIC Man page
canopy.output Man page
canopy.plottree Man page
canopy.post Man page
canopy.sample Man page
getclonalcomposition Man page
getCMCm Man page
getCZ Man page
getlikelihood Man page
getQ Man page
getVAF Man page
getZ Man page
initialcna Man page
initialcnacopy Man page
initialP Man page
initialsna Man page
MDA231 Man page
MDA231_sampchain Man page
MDA231_tree Man page
plotpostlikelihood Man page
sampcna Man page
sampcnacopy Man page
sampP Man page
sampsna Man page
sortcna Man page
toy Man page
toy2 Man page

Files

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

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