argyle: An R Package for Analysis of Illumina Genotyping Arrays

G3 (Bethesda). 2015 Dec 18;6(2):281-6. doi: 10.1534/g3.115.023739.


Genotyping microarrays are an important and widely-used tool in genetics. I present argyle, an R package for analysis of genotyping array data tailored to Illumina arrays. The goal of the argyle package is to provide simple, expressive tools for nonexpert users to perform quality checks and exploratory analyses of genotyping data. To these ends, the package consists of a suite of quality-control functions, normalization procedures, and utilities for visually and statistically summarizing such data. Format-conversion tools allow interoperability with popular software packages for analysis of genetic data including PLINK, R/qtl and DOQTL. Detailed vignettes demonstrating common use cases are included as supporting information. argyle bridges the gap between the low-level tasks of quality control and high-level tasks of genetic analysis. It is freely available at and has been submitted to Bioconductor.

Keywords: SNP microarrays; genotyping; software.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Alleles
  • Computational Biology / methods*
  • Gene Frequency
  • Genotype
  • Genotyping Techniques
  • Humans
  • Oligonucleotide Array Sequence Analysis* / methods
  • Polymorphism, Single Nucleotide
  • Quality Control
  • Reproducibility of Results
  • Software*
  • Web Browser