# Expanding Ploidy and Allele-Frequency on Nested Subpopulations

## Documentation for package ‘expands’ version 2.1.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

assignMutations | Mutation Assignment
assignQuantityToMutation | Quantity assignment (copy number) to mutations
assignQuantityToSP | Quantity assignment (copy number) 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
gatherEXPANDSoutput | Reading EXPANDS' output files
plotSPs | Subpopulation Visualization
roi | Regions of interest
runExPANdS | Main Function
simulation | Simulated heterogeneous samples
snv | Single Nucleotide Variations