snp_readBed {bigsnpr}

Read PLINK files into a "bigSNP"

Description

Functions to read bed/bim/fam files into a bigSNP.

Usage

snp_readBed(bedfile, backingfile = sub_bed(bedfile))

snp_readBed2(
  bedfile,
  backingfile = sub_bed(bedfile),
  ind.row = rows_along(obj.bed),
  ind.col = cols_along(obj.bed),
  ncores = 1
)

Arguments

bedfile

Path to file with extension ".bed" to read. You need the corresponding ".bim" and ".fam" in the same directory.

backingfile

The path (without extension) for the backing files for the cache of the bigSNP object. Default takes the bedfile without the ".bed" extension.

ind.row

An optional vector of the row indices (individuals) that are used. If not specified, all rows are used.
Don't use negative indices.

ind.col

An optional vector of the column indices (SNPs) that are used. If not specified, all columns are used.
Don't use negative indices.

ncores

Number of cores used. Default doesn't use parallelism. You may use nb_cores.

Details

For more information on these formats, please visit PLINK webpage. For other formats, please use PLINK to convert them in bedfiles, which require minimal space to store and are faster to read. For example, to convert from a VCF file, use the --vcf option. See snp_plinkQC.

Value

The path to the RDS file that stores the bigSNP object. Note that this function creates one other file which stores the values of the Filebacked Big Matrix.
You shouldn't read from PLINK files more than once. Instead, use snp_attach to load the "bigSNP" object in any R session from backing files.

Examples

(bedfile <- system.file("extdata", "example.bed", package = "bigsnpr"))

# Reading the bedfile and storing the data in temporary directory
rds <- snp_readBed(bedfile, backingfile = tempfile())

# Loading the data from backing files
test <- snp_attach(rds)

str(test)
dim(G <- test$genotypes)
G[1:8, 1:8]