Performing Highly Efficient Genome Scans for Local Adaptation with R Package pcadapt Version 4
Performing Highly Efficient Genome Scans for Local Adaptation with R Package pcadapt Version 4
复制标题
DOI：
10.1093/molbev/msaa053
复制
发表时间：
2020-07-01
影响因子：
10.7
通讯作者：
Blum, Michael G. B.
中科院分区：
文献类型：
--
作者：
Prive, Florian;Luu, Keurcien;Blum, Michael G. B.
R软件包pcadapt是一个用户友好的R软件包，用于执行基因组扫描以进行局部适应。在这里，我们提出了pcadapt的第4版，它大大提高了计算效率，同时提供了类似的结果。通过使用不同的格式存储基因型和不同的算法计算基因型矩阵的主成分，这是方法pcadapt中计算要求最高的步骤，这种改进是可能的。这些变化被无缝集成到现有的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（在我们的分析中为20-60倍）。
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.