AmplificationTimeR: an R package for timing sequential amplification events

Author:

Jakobsdottir G Maria12ORCID,Dentro Stefan C32,Bristow Robert G142,Wedge David C12ORCID

Affiliation:

1. Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre , Manchester M13 9PL, United Kingdom

2. Christie Hospital, The Christie NHS Foundation Trust, Manchester Academic Health Science Centre , Manchester M20 4BX, United Kingdom

3. Division of AI in Oncology, German Cancer Research Center (DKFZ) , Heidelberg, Germany

4. CRUK Manchester Institute and Manchester Cancer Research Centre , Manchester M20 4GJ, United Kingdom

Abstract

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.

Funder

Cancer Research UK RadNet Manchester

Publisher

Oxford University Press (OUP)

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