write_snp {genio} | R Documentation |
Write Eigenstrat *.snp files
Description
This function writes a tibble with the right columns into a standard Eigenstrat *.snp file.
It uses readr::write_tsv()
to do it efficiently.
Usage
write_snp(file, tib, verbose = TRUE)
Arguments
file |
Output file (whatever is accepted by |
tib |
The tibble or data.frame to write.
It must contain these columns: |
verbose |
If |
Value
The output tib
invisibly (what readr::write_tsv()
returns).
See Also
Eigenstrat SNP format reference: https://github.com/DReichLab/EIG/tree/master/CONVERTF
Examples
# to write an existing table `snp` into file "data.snp", run like this:
# write_snp("data", snp)
# this also works
# write_snp("data.snp", snp)
# 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(
id = 1:3,
chr = 1:3,
posg = 0,
pos = 1:3,
ref = 'A',
alt = 'B'
)
# a dummy file
file_out <- tempfile('delete-me-example', fileext = '.snp') # will also work without extension
# write the table out in *.snp format (no header, columns in right order)
write_snp(file_out, tib)
# delete output when done
file.remove(file_out)