README.md

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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.

Quick demo

LIST OF FEATURES

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.

New! Package {bigsnpr} now provides functions that directly work on bed files with a few missing values. See new paper "Efficient toolkit implementing..".

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:

New! Package {bigsnpr} now provides functions that directly work on bed files with a few missing values. See new 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

How to make a great R reproducible example?

Please open an issue if you find a bug.

If you want help using {bigstatsr}, 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



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bigsnpr documentation built on June 3, 2021, 5:12 p.m.