ensemblQueryR:在R中对Ensembl LD API端点进行快速,灵活和高通量查询
Aine Fairbrother-Browne1,2,3, Sonia García-Ruiz1,4, Regina Hertfelder Reynolds1,4
1Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK.
GigaByte (Hong Kong, China)
|September 21, 2023
概括
ensemblQueryR是一个新的 R 包,用于高效地查询 Ensembl 链接不平衡 (LD) 数据. 与现有工具相比,它提供更快的性能和更少的内存使用,增强高通量遗传分析.
科学领域:
- 遗传学 是一个遗传学.
- 生物信息学是一种生物信息学.
- 计算生物学 计算生物学
背景情况:
- 访问和分析大规模的遗传数据,特别是来自Ensembl的链接不平衡 (LD) 信息,对于人口遗传学和协会研究至关重要.
- 对于查询Ensembl LD端点的现有工具可能是计算密集的,这对高吞吐量分析构成挑战.
研究的目的:
- 推出 ensemblQueryR,一个新的 R 包,旨在高效,用户友好的查询 Ensembl LD 端点.
- 为需要访问 LD 数据的研究人员提供灵活和高通量解决方案.
主要方法:
- 开发一个R包, ensemblQueryR,具有用于单个和多个查询操作的直观功能.
- 实现并行化功能,以优化处理时间,用于大型查询大小.
- 使用Docker和Singularity进行集装箱化,以实现跨平台兼容性.
主要成果:
- 与现有的工具相比,ensemblQueryR显著提高了计算性能,速度提高了10倍,并利用了三分之一的随机存储器 (RAM).
- 该软件包支持用于输入和输出的直观的R对象类型,方便自定义代码集成.
- 平行化选项有效地利用计算资源来实现更快的处理.
结论:
- ensemblQueryR为查询Ensembl LD数据提供了一个快速,内存高效和用户友好的解决方案,适合高通量遗传研究.
- 它的跨平台可访问性通过Docker和Singularity图像扩大了其在各种计算环境中的实用性.
- 预计该工具将加速需要LD信息的基因分析.
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