# snpAIMeR: R package for evaluating ancestry informative marker contributions in non-model population diagnostics

## TL;DR

snpAIMeR is an R package that helps evaluate the usefulness of genetic markers for determining ancestry in non-model populations.

## Contribution

It introduces a user-friendly tool for assessing marker informativeness using cross-validation in non-model systems.

## Key findings

- snpAIMeR uses leave-one-out cross-validation to assess population assignment rates.
- The package helps reduce genotyping effort by identifying informative marker combinations.
- It is designed for non-model systems where marker evaluation resources are limited.

## Abstract

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).