write_bed: Write a genotype matrix into Plink BED format

In genio: Genetics Input/Output Functions

Write a genotype matrix into Plink BED format

Description

This function accepts a standard R matrix containing genotypes (values in c( 0, 1, 2, NA )) and writes it into a Plink-formatted BED (binary) file. Each genotype per locus (m loci) and individual (n total) counts the number of alternative alleles or NA for missing data. No *.fam or *.bim files are created by this basic function.

Usage

write_bed(file, X, verbose = TRUE, append = FALSE)

Arguments

file	Output file path. .bed extension may be omitted (will be added automatically if it is missing).
X	The m-by-n genotype matrix. Row and column names, if present, are ignored.
verbose	If TRUE (default), function reports the path of the file being written (after autocompleting the extension).
append	If TRUE, appends variants onto the file. (Default is FALSE).

Details

Genotypes with values outside of [0, 2] cause an error, in which case the partial output is deleted. However, beware that decimals get truncated internally, so values that truncate to 0, 1, or 2 will not raise errors. The BED format does not accept fractional dosages, so such data will not be written as expected.

Value

Nothing

See Also

write_plink() for writing a set of BED/BIM/FAM files.

Plink BED format reference: https://www.cog-genomics.org/plink/1.9/formats#bed

Examples

# to write an existing matrix `X` into file "data.bed", run like this:
# write_bed("data", X)
# this also works
# write_bed("data.bed", X)

# The following example is more detailed but also more awkward
# because (only for these examples) the package must create the file in a *temporary* location

file_out <- tempfile('delete-me-example', fileext = '.bed') # will also work without extension
# create 10 random genotypes
X <- rbinom(10, 2, 0.5)
# replace 3 random genotypes with missing values
X[sample(10, 3)] <- NA
# turn into 5x2 matrix
X <- matrix(X, nrow = 5, ncol = 2)
# write this data to file in BED format
# (only *.bed gets created, no *.fam or *.bim in this call)
write_bed(file_out, X)
# delete output when done
file.remove(file_out)

genio documentation built on Jan. 7, 2023, 1:12 a.m.