write_bim: Write Plink *.bim files

In genio: Genetics Input/Output Functions

Write Plink *.bim files

Description

This function writes a tibble with the right columns into a standard Plink *.bim file. It uses readr::write_tsv() to do it efficiently.

Usage

write_bim(file, tib, verbose = TRUE, append = FALSE)

Arguments

file	Output file (whatever is accepted by readr::write_tsv()). If file is missing the expected *.bim extension, the function adds it.
tib	The tibble or data.frame to write. It must contain these columns: chr, id, posg, pos, alt, ref. Throws an error if any of these columns are missing. Additional columns are ignored. Columns are automatically reordered in output as expected in format.
verbose	If TRUE (default), function reports the path of the file being written (after autocompleting the extension).
append	If TRUE, appends rows onto the file. (Default is FALSE).

Value

The output tib invisibly (what readr::write_tsv() returns).

See Also

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

Plink BIM format references: https://www.cog-genomics.org/plink/1.9/formats#bim https://www.cog-genomics.org/plink/2.0/formats#bim

Examples

# to write an existing table `bim` into file "data.bim", run like this:
# write_bim("data", bim)
# this also works
# write_bim("data.bim", bim)

# 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

# create a dummy tibble with the right columns
library(tibble)
tib <- tibble(
    chr = 1:3,
    id = 1:3,
    posg = 0,
    pos = 1:3,
    alt = 'B',
    ref = 'A'
)
# a dummy file
file_out <- tempfile('delete-me-example', fileext = '.bim') # will also work without extension
# write the table out in *.bim format (no header, columns in right order)
write_bim(file_out, tib)

# example cleanup
file.remove(file_out)

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