Expanding Ploidy and Allele-Frequency on Nested Subpopulations


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Documentation for package ‘expands’ version 1.7.2

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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 for a single mutation.
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