AmplificationTimeR：一个用于定时序扩增事件的 R 包。

AmplificationTimeR: an R package for timing sequential amplification events.

机构信息

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.

出版信息

Bioinformatics. 2024 Jun 3;40(6). doi: 10.1093/bioinformatics/btae281.

DOI:10.1093/bioinformatics/btae281

PMID:38656989

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11153944/

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.

摘要

动机

在局灶扩增区域中，几乎没有方法可以对个体扩增事件进行定时。目前的方法在能够定时的拷贝数状态方面也受到限制。在这里，我们引入了 AmplificationTimeR，这是一种用于对经历了单增益和全基因组复制的区域进行更高水平的拷贝数增益定时并推断事件最简约顺序的方法。我们的方法是对基因组增益定时的既定方法的扩展。