FnR: R包用于计算内生和计数器关系系数
1Livestock Improvement Corporation, Private Bag 3016, Hamilton, 3240, New Zealand. mohammad.nilforooshan@lic.co.nz.
BMC ecology and evolution
|July 18, 2024
概括
R包FnR有效计算动物关系系数,这对于保护和繁殖计划至关重要. 这种免费的开源软件通过最大限度地减少内生繁殖和最大限度地提高大型数据集的有效种群规模来优化交配计划.
科学领域:
- 动物遗传学和动物基因组学
- 定量遗传学 是一种定量遗传学.
- 保护生物学 保护生物学
背景情况:
- 亲生繁殖和关系系数对于有效的动物繁殖和保护策略至关重要.
- 监测内生繁殖率和优化交配计划对于小型保护和大型商业种群都至关重要.
- 高效,免费和开源软件可以显著帮助研究人员和学生在这些努力.
研究的目的:
- 引入一个高效的R包 (FnR) 用于计算计数器关系系数.
- 解决确定关系的计算挑战,特别是当后代数据有限时.
- 提供一种工具,尽量减少内生繁殖,最大限度地提高动物种群的有效种群规模.
主要方法:
- 这项研究使用了一个R包,通过引入人造后代来计算关系系数,用于在血统中缺乏直接后代的个体.
- 基准测试涉及计算大型数据集的关系系数 (在超过270万的血统中最多800只动物).
- 运行时间和内存使用在不同的场景下进行了评估,包括预先计算的同胞系数和D的对角元素.
主要成果:
- 在标准硬件上,FnR包表现出高效率,在几分钟内计算出20万个关系系数.
- 通过提供预先计算的近亲繁殖系数 (减少超过65%的运行时间) 和D的对角元素 (进一步减少) 来显著提高性能.
- 该软件显示内存使用量很低,在仅有1GB内存的机器上进行分析.
结论:
- R包FnR是一个节省时间和内存的,免费的,开源的工具,有利于大规模的保护和繁殖计划.
- 建议保存最新的近亲繁殖系数估计值,以恢复新动物的计算.
- 从头开始计算'd'系数是快速的,这表明存储它们以供将来使用的好处很小.
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