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bigsnpr

{bigsnpr} is an R package for the analysis of massive SNP arrays, primarily designed for human genetics. It enhances the features of package {bigstatsr} for the purpose of analyzing genotype data.

To get you started:

Installation

In R, run

# install.packages("remotes")
remotes::install_github("privefl/bigsnpr")

or for the CRAN version

install.packages("bigsnpr")

Input formats

This package reads bed/bim/fam files (PLINK preferred format) using functions snp_readBed() and snp_readBed2(). Before reading into this package’s special format, quality control and conversion can be done using PLINK, which can be called directly from R using snp_plinkQC() and snp_plinkKINGQC().

This package can also read UK Biobank BGEN files using function snp_readBGEN(). This function takes around 40 minutes to read 1M variants for 400K individuals using 15 cores.

This package uses a class called bigSNP for representing SNP data. A bigSNP object is a list with some elements:

Note that most of the algorithms of this package don’t handle missing values. You can use snp_fastImpute() (taking a few hours for a chip of 15K x 300K) and snp_fastImputeSimple() (taking a few minutes only) to impute missing values of genotyped variants.

Package {bigsnpr} also provides functions that directly work on bed files with a few missing values (the bed_*() functions). See paper “Efficient toolkit implementing..”.

Polygenic scores

Polygenic scores are one of the main focus of this package. There are 3 main methods currently available:

Possible upcoming features

You can request some feature by opening an issue.

Bug report / Support

How to make a great R reproducible example?

Please open an issue if you find a bug.

If you want help using {bigstatsr} (the big_*() functions), please open an issue on {bigstatsr}’s repo, or post on Stack Overflow with the tag bigstatsr.

I will always redirect you to GitHub issues if you email me, so that others can benefit from our discussion.

References

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.