expands: Expanding Ploidy and Allele-Frequency on Nested Subpopulations
Version 2.0.0

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 (). 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 .

Getting started

Package details

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

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expands documentation built on May 30, 2017, 5:08 a.m.