Expanding Ploidy and Allele-Frequency on Nested Subpopulations


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Documentation for package ‘expands’ version 1.6.1

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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
snv Single Nucleotide Variations