Thumbnail Image
Publication

AmplificationTimeR: an R package for timing sequential amplification events

Jakobsdottir, Maria G
; 
Dentro, Stefan C
; 
Bristow, Robrert G
; 
Wedge, David C
Citations
Altmetric:
Abstract
MOTIVATION: Few methods exist for timing individual amplification events in regions of focal amplification. Current methods are also limited in the copy number states that they are able to time. Here we introduce AmplificationTimeR, a method for timing higher level copy number gains and inferring the most parsimonious order of events for regions that have undergone both single gains and whole genome duplication. Our method is an extension of established approaches for timing genomic gains. RESULTS: We can time more copy number states, and in states covered by other methods our results are comparable to previously published methods. AVAILABILITY AND IMPLEMENTATION: AmplificationTimer is freely available as an R package hosted at https://github.com/Wedge-lab/AmplificationTimeR.
Authors
Jakobsdottir, Maria G
Dentro, Stefan C
Bristow, Robrert G
Wedge, David C
Affiliation
Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PL, United Kingdom. Christie Hospital, The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M20 4BX, United Kingdom. CRUK Manchester Institute and Manchester Cancer Research Centre, Manchester M20 4GJ, United Kingdom.
Description
Date
2024
Publisher
Collections
All Christie Publications
Show all metadata
Files
Thumbnail Image
Found with Open Access Button
Adobe PDF, 10.86 MB
Keywords
Type
Article
Citation
Jakobsdottir GM, Dentro SC, Bristow RG, Wedge DC. AmplificationTimeR: an R package for timing sequential amplification events. Bioinformatics (Oxford, England). 2024 Jun 3;40(6). PubMed PMID: 38656989. Pubmed Central PMCID: PMC11153944. Epub 2024/04/24. eng.
Journal Title
Journal ISSN
Volume Title
URI
http://hdl.handle.net/10541/627034
Embedded videos