| 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 |
| 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 |