expands: Expanding Ploidy and Allele-Frequency on Nested Subpopulations

Expanding Ploidy and Allele Frequency on Nested Subpopulations (expands) characterizes coexisting subpopulations in a single tumor sample using copy number and allele frequencies derived from exome- or whole genome sequencing input data (<http://www.ncbi.nlm.nih.gov/pubmed/24177718>). The model detects coexisting genotypes by leveraging run-specific tradeoffs between depth of coverage and breadth of coverage. This package predicts the number of clonal expansions, the size of the resulting subpopulations in the tumor bulk, the mutations specific to each subpopulation, tumor purity and phylogeny. The main function runExPANdS() provides the complete functionality needed to predict coexisting subpopulations from single nucleotide variations (SNVs) and associated copy numbers. The robustness of subpopulation predictions increases with the number of mutations provided. It is recommended that at least 200 mutations are used as input to obtain stable results. Updates in version 2.0 include: (i) copy-neutral LOH are now modelled; (ii) more robust calculation of cell frequency probabilities from kernel density estimates instead of Gaussian mixtures. Further documentation and FAQ available at <http://dna-discovery.stanford.edu/software/expands>.

Install the latest version of this package by entering the following in R:
install.packages("expands")
AuthorNoemi Andor
Date of publication2017-04-09 17:49:01 UTC
MaintainerNoemi Andor <expands.r@gmail.com>
LicenseGPL-2
Version2.0.0
http://dna-discovery.stanford.edu/software/expands, https://github.com/noemiandor/expands, https://groups.google.com/d/forum/expands

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Files

inst
inst/java
inst/java/expands.jar
inst/doc
inst/doc/expands.R
inst/doc/expands.Rnw
inst/doc/expands.pdf
NAMESPACE
NEWS.md
data
data/cbs.rda
data/simulation.rda
data/snv.rda
R
R/assignQuantityToMutation.R R/runExPANdS.R R/onLoad.R R/assignMutations.R R/clusterCellFrequencies.R
R/sysdata.rda
R/buildMultiSamplePhylo.R R/plotSPs.R R/addColumn.R R/cellfrequency_pdf.R R/computeCellFrequencyDistributions.R R/readSNVandCBS.R R/buildPhylo.R R/assignQuantityToSP.R
vignettes
vignettes/expands.bib
vignettes/expands.Rnw
vignettes/ID_MRD_001_primPancreas.sps
vignettes/ID_MRD_001_metLung.sps
vignettes/ID_MRD_001_metLung.cbs
vignettes/ID_MRD_001_primPancreas.cbs
vignettes/ID_MRD_001_metKidney.cbs
vignettes/ID_MRD_001_metKidney.sps
MD5
java
java/src
java/src/core
java/src/core/ParallelSubpopulations.java
java/src/core/Subpopulation.java
java/src/core/utils
java/src/core/utils/NotAValidCompositionException.java
java/src/core/utils/AFtimesCopyNumber.java
java/src/core/utils/CopyNumber.java
java/src/core/utils/Common.java
java/src/core/utils/Measurement.java
java/lib
java/lib/commons-math3-3.0.jar
java/uml
java/uml/ParallelSubpopulations.tif
java/uml/expands2.tif
java/uml/EXPANDS.mdzip
build
build/vignette.rds
DESCRIPTION
man
man/cbs.Rd man/assignQuantityToSP.Rd man/simulation.Rd man/runExPANdS.Rd man/buildMultiSamplePhylo.Rd man/cellfrequency_pdf.Rd man/assignQuantityToMutation.Rd man/snv.Rd man/clusterCellFrequencies.Rd man/plotSPs.Rd man/computeCellFrequencyDistributions.Rd man/assignMutations.Rd man/roi.Rd man/buildPhylo.Rd

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