ioncopy: Calling Copy Number Alterations in Amplicon Sequencing Data

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.

Author
Jan Budczies
Date of publication
2015-08-26 14:53:52
Maintainer
Jan Budczies <jan.budczies@charite.de>
License
GPL-3
Version
1.0

View on CRAN

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

Files in this package

ioncopy
ioncopy/NAMESPACE
ioncopy/data
ioncopy/data/coverage.rda
ioncopy/R
ioncopy/R/calculate.CN.R
ioncopy/R/call.genes.R
ioncopy/R/ioncopy-internal.R
ioncopy/R/call.amplicons.R
ioncopy/MD5
ioncopy/DESCRIPTION
ioncopy/man
ioncopy/man/calculate.CN.Rd
ioncopy/man/ioncopy-package.Rd
ioncopy/man/coverage.Rd
ioncopy/man/call.amplicons.Rd
ioncopy/man/call.genes.Rd