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. 2019 May 7;9(5):1377-1383.
doi: 10.1534/g3.119.400018.

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

Alexander Grueneberg  1 , Gustavo de Los Campos  1   2   3
Affiliations

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

Alexander Grueneberg et al. G3 (Bethesda). .

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.

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Figures

Figure 1
Figure 1
Manhattan plot obtained by regressing sex-age adjusted height on variants using data from the training set (n = 222,648, unrelated White British).
Figure 2
Figure 2
Correlation (+/− SE) between sex-adjusted height and predicted height in the testing set, by the number of SNPs used.
See this image and copyright information in PMC

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