Hemstrom William, Jones Melissa
Department of Animal Science, University of California, Davis, California, USA.
Mol Ecol Resour. 2023 May;23(4):962-973. doi: 10.1111/1755-0998.13721. Epub 2022 Nov 25.
The analysis of genomic data can be an intimidating process, particularly for researchers who are not experienced programmers. Commonly used analyses are spread across many programs, each requiring their own specific input formats, and so data must often be repeatedly reorganized and transformed into new formats. Analyses often require splitting data according to metadata variables such as population or family, which can be challenging to manage in large data sets. Here, we introduce snpR, a user-friendly data analysis package in R for processing SNP genomic data. snpR is designed to automate data subsetting and analyses across categorical metadata while also streamlining repeated analyses by integrating approaches contained in many different packages in a single ecosystem. snpR facilitates iterative and efficient analyses centred on a single R object for an entire analysis pipeline.
基因组数据分析可能是一个令人生畏的过程，尤其是对于没有经验的程序员的研究人员来说。常用的分析分布在许多程序中，每个程序都需要自己特定的输入格式，因此数据通常必须反复重新组织并转换为新格式。分析通常需要根据诸如人群或家族等元数据变量对数据进行拆分，这在大型数据集中可能具有挑战性。在这里，我们介绍snpR，这是一个R语言中用于处理SNP基因组数据的用户友好型数据分析包。snpR旨在自动进行跨分类元数据的数据子集划分和分析，同时通过在单个生态系统中集成许多不同软件包中包含的方法来简化重复分析。snpR有助于以单个R对象为中心进行迭代和高效分析，用于整个分析流程。
