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G3 (Bethesda). 2019 Mar 20. pii: g3.400018.2019. doi: 10.1534/g3.119.400018. [Epub ahead of print]

BGData - A Suite of R Packages for Genomic Analysis with Big Data.

Author information

1
Michigan State University gruenebe@msu.edu.
2
Michigan State University.

Abstract

We created a suite of packages to enable analysis of extremely large genomic data sets (potentially millions of individuals and millions of molecular markers) within the R environment. The package offers: a matrix-like interface for .bed files (PLINK's binary format for genotype data), a novel class of linked arrays that allows linking data stored in multiple files to form a single array accessible from the R computing environment, methods for parallel computing capabilities that can carry out computations on very large data sets without loading the entire data into memory and a basic set of methods for statistical genetic analyses. The package is accessible through CRAN and GitHub. In this note, we describe the classes and methods implemented in each of the packages that make the suite and illustrate the use of the packages using data from the UK Biobank.

KEYWORDS:

big data; biobank; distributed computing; genetic analyses; parallel computing

PMID:
30894453
DOI:
10.1534/g3.119.400018
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