Finding Recurrent DNA Copy Number Alterations and Differences


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Documentation for package ‘DiNAMIC.Duo’ version 1.0.2

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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