{bignspr} 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

Installation

devtools::install_github("privefl/bigsnpr")

Input formats

This package reads bed/bim/fam files (PLINK preferred format) using function snp_readBed(). 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_plinkIBDQC.

This package now also reads UK Biobank BGEN files using function snp_readBGEN().

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

  • genotypes: A FBM.code256. Rows are samples and columns are SNPs. This stores genotypes calls or dosages (rounded to 2 decimal places).
  • fam: A data.frame containing some information on the SNPs.
  • map: A data.frame giving some information on the individuals.

Possible upcoming features

You can request some feature by opening an issue.

Bug report

Please open an issue if you find a bug.

If you want help using {bigstatsr}, please post on Stack Overflow with the tag bigstatsr.

How to make a great R reproducible example?

Get genes associated with SNPs

devtools::source_gist("42b41d771bbeae63245b8304ef283c70", filename = "get-genes.R")
rsid <- c("rs3934834", "rs3737728", "rs6687776", "rs9651273", "rs4970405",
          "rs12726255", "rs2298217", "rs4970362", "rs9660710", "rs4970420")
snp_gene(rsid)