ioncopy: Calling Copy Number Alterations in Amplicon Sequencing Data
Version 1.0

Method for the calculation of copy numbers and calling of copy number alterations. The algorithm uses coverage data from amplicon sequencing of a sample cohort as input. The method includes significance assessment, correction for multiple testing and does not depend on normal DNA controls.

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AuthorJan Budczies
Date of publication2015-08-26 14:53:52
MaintainerJan Budczies <jan.budczies@charite.de>
LicenseGPL-3
Version1.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("ioncopy")

Man pages

calculate.CN: Calculation of copy numbers
call.amplicons: Amplicon-wise call of copy number alterations
call.genes: Gene-wise calling of copy number alterations
coverage: Coverage data of 154 amplicons in 184 breast carcinomas
ioncopy-package: Calling copy number alterations in amplicon sequencing data

Functions

calculate.CN Man page Source code
call.amplicons Man page Source code
call.genes Man page Source code
coverage Man page
ioncopy Man page
ioncopy-package Man page

Files

NAMESPACE
data
data/coverage.rda
R
R/calculate.CN.R
R/call.genes.R
R/ioncopy-internal.R
R/call.amplicons.R
MD5
DESCRIPTION
man
man/calculate.CN.Rd
man/ioncopy-package.Rd
man/coverage.Rd
man/call.amplicons.Rd
man/call.genes.Rd
ioncopy documentation built on May 29, 2017, 9:03 a.m.