G. M. Jakobsdottir, Stefan C Dentro, Robert G Bristow, David C Wedge
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引用次数: 0
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
AmplificationTimer is freely available as an R package hosted at https://github.com/Wedge-lab/AmplificationTimeR.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
动机目前很少有方法能对病灶扩增区域的单个扩增事件进行计时。目前的方法在能够计时的拷贝数状态方面也受到限制。在此，我们介绍 AmplificationTimeR，这是一种为更高水平的拷贝数增殖计时的方法，并能推断出经历过单个增殖和全基因组复制的区域的最合理的事件顺序。我们的方法是对已有的基因组增殖计时方法的扩展。结果我们可以对更多的拷贝数状态进行计时，而且在其他方法所涵盖的状态下，我们的结果与之前发表的方法相当。AVILABILITYAmplificationTimer 是一个 R 包，可免费获取，托管在 https://github.com/Wedge-lab/AmplificationTimeR.SUPPLEMENTARY INFORMATIONSupplementary data are available at Bioinformatics online.
期刊介绍：
The leading journal in its field, Bioinformatics publishes the highest quality scientific papers and review articles of interest to academic and industrial researchers. Its main focus is on new developments in genome bioinformatics and computational biology. Two distinct sections within the journal - Discovery Notes and Application Notes- focus on shorter papers; the former reporting biologically interesting discoveries using computational methods, the latter exploring the applications used for experiments.
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