argyle: An R Package for Analysis of Illumina Genotyping Arrays | Zendy

Andrew P. Morgan | Zendy

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argyle: An R Package for Analysis of Illumina Genotyping Arrays

Author(s) -

Andrew P. Morgan

Publication year - 2015

Publication title -

g3 genes genomes genetics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 1.468

H-Index - 66

ISSN - 2160-1836

DOI - 10.1534/g3.115.023739

Subject(s) - bioconductor , computer science , r package , genotyping , suite , normalization (sociology) , software , interoperability , data mining , biology , world wide web , genotype , programming language , genetics , history , archaeology , sociology , gene , anthropology

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 https://github.com/andrewparkermorgan/argyle and has been submitted to Bioconductor.

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