Write PLINK files from a "bigSNP"
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))
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. |
ind.col |
An optional vector of the column indices (SNPs) that are used.
If not specified, all columns are used. |
The input bedfile path.
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$genotypes[]) all.equal(fake$fam, fake2$fam) all.equal(fake$map, fake2$map) # Two different backingfiles fake$genotypes$backingfile fake2$genotypes$backingfile
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