assignPOP: An R package for population assignment using genetic, non-genetic, or integrated data in a machine-learning framework
assignPOP: An R package for population assignment using genetic, non-genetic, or integrated data in a machine-learning framework
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DOI：
10.1111/2041-210x.12897
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发表时间：
2018-02-01
影响因子：
6.6
通讯作者：
Ludsin, Stuart A.
中科院分区：
文献类型：
--
作者：
Chen, Kuan-Yu;Marschall, Elizabeth A.;Ludsin, Stuart A.
1.生物标志物（例如，遗传、微化学和形态特征）来区分个体并将其分配到种群中，可以促进我们理解种群结构和人口统计学的能力，从而有利于物种的保护和管理。缺乏可以评估大型基因组数据集用于群体歧视和分配的可靠性以及允许其与用于相同目的的非遗传标记整合的工具。我们的R包assignPOP在监督机器学习框架中提供了这两个函数。assignPOP使用蒙特-卡罗和K折交叉验证程序，以及主成分分析，使用训练（即，基线源群体）和测试（即，验证）独立的数据集。然后，用户可以根据这些数据集的相对大小和分类函数建立指定的预测模型，包括线性判别分析，支持向量机，朴素贝叶斯，决策树和随机森林。4. assignPOP可以使任何寻求使用遗传或非遗传数据来推断人口结构和个体成员的研究人员受益。assignPOP是GPL许可证下的免费R软件包，可以从CRAN或下载。也可以在https://github.com/alexkychen/assignPOP上找到全面的教程。也可以在https://alexkychen.github.io/assignPOP/上找到全面的教程。
1. The use of biomarkers (e.g., genetic, microchemical and morphometric characteristics) to discriminate among and assign individuals to a population can benefit species conservation and management by facilitating our ability to understand population structure and demography.2. Tools that can evaluate the reliability of large genomic datasets for population discrimination and assignment, as well as allow their integration with non-genetic markers for the same purpose, are lacking. Our R package, assignPOP, provides both functions in a supervised machine-learning framework.3. assignPOP uses Monte-Carlo and K-fold cross-validation procedures, as well as principal component analysis, to estimate assignment accuracy and membership probabilities, using training (i.e., baseline source population) and test (i.e., validation) datasets that are independent. A user then can build a specified predictive model based on the relative sizes of these datasets and classification functions, including linear discriminant analysis, support vector machine, naive Bayes, decision tree and random forest.4. assignPOP can benefit any researcher who seeks to use genetic or non-genetic data to infer population structure and membership of individuals. assignPOP is a freely available R package under the GPL license, and can be downloaded from CRAN or at . A comprehensive tutorial can also be found at https://github.com/alexkychen/assignPOP. A comprehensive tutorial can also be found at https://alexkychen.github.io/assignPOP/.