snp_writeBed: Write PLINK files from a "bigSNP"

In bigsnpr: Analysis of Massive SNP Arrays

Write PLINK files from a "bigSNP"

Description

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

Usage

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[])
all.equal(fake$fam, fake2$fam)
all.equal(fake$map, fake2$map)

# Two different backingfiles
fake$genotypes$backingfile
fake2$genotypes$backingfile

bigsnpr documentation built on Sept. 30, 2024, 9:18 a.m.