National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark.
University of Grenoble Alpes, Laboratoire TIMC-IMAG, UMR 5525, La Tronche, France.
Mol Biol Evol. 2020 Jul 1;37(7):2153-2154. doi: 10.1093/molbev/msaa053.
R package pcadapt is a user-friendly R package for performing genome scans for local adaptation. Here, we present version 4 of pcadapt which substantially improves computational efficiency while providing similar results. This improvement is made possible by using a different format for storing genotypes and a different algorithm for computing principal components of the genotype matrix, which is the most computationally demanding step in method pcadapt. These changes are seamlessly integrated into the existing pcadapt package, and users will experience a large reduction in computation time (by a factor of 20-60 in our analyses) as compared with previous versions.
R 包 pcadapt 是一个用户友好的 R 包，用于进行基因组扫描以检测局部适应性。在这里，我们介绍了 pcadapt 的 4 版本，它在提供类似结果的同时，大大提高了计算效率。这一改进是通过使用存储基因型的不同格式和计算基因型矩阵主成分的不同算法实现的，而这是方法 pcadapt 中计算最耗时的步骤。这些更改无缝集成到现有的 pcadapt 包中，与以前的版本相比，用户将体验到计算时间的大幅减少（在我们的分析中减少 20-60 倍）。
