Package: Canopy 1.3.0

Yuchao Jiang

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.

Authors:Yuchao Jiang, Nancy R. Zhang

Canopy_1.3.0.tar.gz
Canopy_1.3.0.zip(r-4.5)Canopy_1.3.0.zip(r-4.4)Canopy_1.3.0.zip(r-4.3)
Canopy_1.3.0.tgz(r-4.4-any)Canopy_1.3.0.tgz(r-4.3-any)
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Canopy.pdf |Canopy.html✨
Canopy/json (API)
NEWS

# Install 'Canopy' in R:
install.packages('Canopy', repos = c('https://yuchaojiang.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/yuchaojiang/canopy/issues

Datasets:
  • AML43 - SNA input for primary tumor and relapse genome of leukemia patient from Ding et al. Nature 2012.
  • MDA231 - Dataset for project MDA231
  • MDA231_sampchain - List of pre-sampled trees
  • MDA231_tree - Most likely tree from project MDA231
  • toy - Toy dataset for Canopy
  • toy2 - Toy dataset 2 for Canopy
  • toy3 - Toy dataset 3 for Canopy

On CRAN:

30 exports 4.37 score 24 dependencies 41 mentions 65 scripts 205 downloads

Last updated 7 years agofrom:c22e96c142. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 17 2024
R-4.5-winOKSep 17 2024
R-4.5-linuxOKSep 17 2024
R-4.4-winOKSep 17 2024
R-4.4-macOKSep 17 2024
R-4.3-winOKSep 17 2024
R-4.3-macOKSep 17 2024

Exports:addsamptreecanopy.BICcanopy.clustercanopy.cluster.Estepcanopy.cluster.Mstepcanopy.outputcanopy.plottreecanopy.postcanopy.samplecanopy.sample.clustercanopy.sample.cluster.nocnacanopy.sample.nocnagetclonalcompositiongetCMCmgetCZgetlikelihoodgetlikelihood.snagetQgetVAFgetZinitialcnainitialcnacopyinitialPinitialsnasampcnasampcnacopysampPsampsnasampsna.clustersortcna

Dependencies:apeclicolorspacedigestdotCall64farverfieldsgluegtablelabelinglatticelifecyclemapsmunsellnlmepheatmapR6RColorBrewerRcpprlangscalesscatterplot3dspamviridisLite

Using Canopy

Rendered fromCanopy_vignettes.Rnwusingutils::Sweaveon Sep 17 2024.

Last update: 2017-12-18
Started: 2015-10-29

Readme and manuals

Help Manual

Help pageTopics
To determine whether the sampled tree will be acceptedaddsamptree
SNA input for primary tumor and relapse genome of leukemia patient from Ding et al. Nature 2012.AML43
To get BIC as a model selection criterioncanopy.BIC
EM algorithm for multivariate clustering of SNAscanopy.cluster
E-step of EM algorithm for multivariate clustering of SNAscanopy.cluster.Estep
M-step of EM algorithm for multivariate clustering of SNAscanopy.cluster.Mstep
To generate a posterior treecanopy.output
To plot tree inferred by Canopycanopy.plottree
Posterior evaluation of MCMC sampled treescanopy.post
MCMC sampling in tree spacecanopy.sample
MCMC sampling in tree space with pre-clustering of SNAscanopy.sample.cluster
MCMC sampling in tree space with pre-clustering of SNAscanopy.sample.cluster.nocna
MCMC sampling in tree spacecanopy.sample.nocna
To get clonal compositiongetclonalcomposition
To get major and minor copy per clonegetCMCm
To get CNA genotyping matrix CZgetCZ
To get likelihood of the treegetlikelihood
To get SNA likelihood of the treegetlikelihood.sna
To get SNA-CNA genotyping matrixgetQ
To get variant allele frequency (VAF)getVAF
To get SNA genotyping matrix ZgetZ
To initialize positions of CNAsinitialcna
To initialize major and minor copies of CNAsinitialcnacopy
To initialize clonal frequency matrixinitialP
To initialize positions of SNAsinitialsna
Dataset for project MDA231MDA231
List of pre-sampled treesMDA231_sampchain
Most likely tree from project MDA231MDA231_tree
To sample CNA positionssampcna
To sample major and minor copies of CNAssampcnacopy
To sample clonal frequencysampP
To sample SNA positionssampsna
To sample positions of SNA clusterssampsna.cluster
To sort identified overlapping CNAs.sortcna
Toy dataset for Canopytoy
Toy dataset 2 for Canopytoy2
Toy dataset 3 for Canopytoy3