AmplificationTimeR: an R Package for Timing Sequential Amplification Events

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2024 Apr 24

PMID 38656989

Authors

G Maria Jakobsdottir

Stefan C Dentro

Robert G Bristow

David C Wedge

Affiliations

Soon will be listed here.

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.

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