bignspr is an R Package for the analysis of massive SNP arrays. It enhances the features of package bigstatsr for the purpose of analysing genotype data.
# Not on CRAN for now because of download_plink() # For the current version devtools::install_github("privefl/bigsnpr")
For now, this package only read bed/bim/fam files (PLINK preferred format) using
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
I use a class called
bigSNP for representing infos on massive SNP arrays. One
bigSNP has at least 3 elements:
FBM.code256. Rows are samples and columns are SNPs. This corresponds to the “bed” file, but each element is encoded on 8 bits rather than only 2 bits for PLINK binary files, which allows for storing more information, without taking too much disk space.
data.framecontaining some information on the SNPs (read from the “.fam” file).
data.framegiving some information on the individuals (read from the “.bim” file).
devtools::source_gist("42b41d771bbeae63245b8304ef283c70", filename = "get-genes.R") rsid <- c("rs3934834", "rs3737728", "rs6687776", "rs9651273", "rs4970405", "rs12726255", "rs2298217", "rs4970362", "rs9660710", "rs4970420") snp_gene(rsid)
Please open an issue if you find a bug. If you want help using bigstatsr, please post on Stack Overflow with the tag bigstatsr (not yet created). How to make a great R reproducible example?