# Finding Recurrent DNA Copy Number Alterations and Differences

## Documentation for package ‘DiNAMIC.Duo’ version 1.0.4

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

cyclicNullR | Create a cyclic shift-based null distribution for one or two copy number matrices
cyclicShiftColR | Perform the cyclic shift procedure on the columns of a matrix
dataPrep | Prepare copy number data for downstream analysis
findNull | Find DiNAMIC's null distribution
genomeChrPlot | A Function for Plotting Mean Copy Number Values and Differences Across Multiple Chromosomes
genomePlot | A Function for Plotting Mean Copy Number Values and Differences Across the Genome
luadSubset | DNA copy number data for lung adenocarcinoma.
luscSubset | DNA copy number data for lung squamous cell carcinoma.
pD | Prepped data for DiNAMIC.Duo.
peelingOne | A Function to Apply the Peeling Algorithm in a Single Copy Number Matrix
peelingOneIterate | A Function to Apply the Peeling Algorithm in a Single Copy Number Matrix
peelingTwo | A Function to Apply the Peeling Algorithm in a Two Copy Number Matrices
peelingTwoIterate | A Function to Apply the Peeling Algorithm for Two Copy Number Matrices
resultsProcess | Processing peeling results