Function to write bed/bim/fam files from a bigSNP. This will use the slot code rounded to write 0s, 1s, 2s or NAs.

snp_writeBed(x, bedfile, ind.row = rows_along(G), ind.col = cols_along(G))

Arguments

x

A bigSNP.

bedfile

Path to file with extension ".bed" to create.

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.

Value

The input bedfile path.

Examples

N <- 17 M <- 911 fake <- snp_fake(N, M) G <- fake$genotypes G[] <- sample(as.raw(0:3), size = length(G), replace = TRUE) # Write the object as a bed/bim/fam object tmp <- tempfile(fileext = ".bed") bed <- snp_writeBed(fake, tmp) # Read this new file for the first time rds <- snp_readBed(bed, backingfile = tempfile()) # Attach object in R session fake2 <- snp_attach(rds) # Same content all.equal(fake$genotypes[], fake2$genotypes[])
#> [1] TRUE
all.equal(fake$fam, fake2$fam)
#> [1] TRUE
all.equal(fake$map, fake2$map)
#> [1] TRUE
# Two different backingfiles fake$genotypes$backingfile
#> [1] "C:\\Users\\au639593\\AppData\\Local\\Temp\\RtmpywXbMx\\file4aa81f4361a9.bk"
fake2$genotypes$backingfile
#> [1] "C:\\Users\\au639593\\AppData\\Local\\Temp\\RtmpywXbMx\\file4aa83501334d.bk"