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>.
|Date of publication||2017-04-09 17:49:01 UTC|
|Maintainer||Noemi Andor <firstname.lastname@example.org>|
|http://dna-discovery.stanford.edu/software/expands, https://github.com/noemiandor/expands, https://groups.google.com/d/forum/expands|
assignMutations: Mutation Assignment
assignQuantityToMutation: Quantity assignment (copy number) to mutations
assignQuantityToSP: Quantity assignment (ploidy) to subpopulations
buildMultiSamplePhylo: Relations between inter- and intra-sample subpopulations
buildPhylo: Relations between subpopulations
cbs: Matrix of copy number fragments
cellfrequency_pdf: Computes the probability distribution of cellular frequencies...
clusterCellFrequencies: Clustering of cellular frequency probability distributions
computeCellFrequencyDistributions: Gathering of cell frequency probability distributions
plotSPs: Subpopulation Visualization
roi: Regions of interest
runExPANdS: Main Function
simulation: Simulated heterogeneous samples
snv: Single Nucleotide Variations
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