Calling Copy Number Alterations in Amplicon Sequencing Data

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Documentation for package ‘ioncopy’ version 2.2.2

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

Help Pages

ioncopy-package	Calling copy number alterations in amplicon sequencing data
assess.CNA	Significance assessment of copy number alterations
calculate.CN	Calculation of copy numbers
call.CNA	Gene-wise or amplicon-wise calling of copy number alterations
coverage	Coverage data of 154 amplicons in 184 breast carcinomas
heatmap.CNA	Visualization of Copy Number and CNA Calls
ioncopy	Calling copy number alterations in amplicon sequencing data
read.coverages	Helper function to read coverages from file system
runIoncopy	Shiny app for Ioncopy
summarize.CNA	Summary of CNA calls