Department of Entomology, University of Kentucky, Lexington, KY 40546, United States.
Bioinformatics. 2024 Jun 3;40(6). doi: 10.1093/bioinformatics/btae377.
Single nucleotide polymorphism (SNP) markers are increasingly popular for population genomics and inferring ancestry for individuals of unknown origin. Because large SNP datasets are impractical for rapid and routine analysis, diagnostics rely on panels of highly informative markers. Strategies exist for selecting these markers, however, resources for efficiently evaluating their performance are limited for non-model systems.
snpAIMeR is a user-friendly R package that evaluates the efficacy of genomic markers for the cluster assignment of unknown individuals. It is intended to help minimize panel size and genotyping effort by determining the informativeness of candidate diagnostic markers. Provided genotype data from individuals of known origin, it uses leave-one-out cross-validation to determine population assignment rates for individual markers and marker combinations.
snpAIMeR is available on CRAN (https://CRAN.R-project.org/package=snpAIMeR).
单核苷酸多态性（SNP）标记物越来越受到人群基因组学和推断未知来源个体的祖先的欢迎。由于大型 SNP 数据集不适用于快速和常规分析，因此诊断依赖于高度信息标记物的面板。存在用于选择这些标记物的策略，但是，对于非模型系统，用于有效评估其性能的资源是有限的。
snpAIMeR 是一个用户友好的 R 包，用于评估基因组标记物对未知个体聚类分配的功效。它旨在通过确定候选诊断标记物的信息量来帮助最小化面板大小和基因分型工作。提供来自已知来源个体的基因型数据，它使用留一法交叉验证来确定个体标记和标记组合的群体分配率。
snpAIMeR 可在 CRAN（https://CRAN.R-project.org/package=snpAIMeR）上获得。
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