Finding Recurrent DNA Copy Number Alterations and Differences

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Documentation for package ‘DiNAMIC.Duo’ version 1.0.2

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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
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