R/write_snp.R

In OchoaLab/genio: Genetics Input/Output Functions

#' Write Eigenstrat *.snp files
#' 
#' This function writes a tibble with the right columns into a standard Eigenstrat *.snp file.
#' It uses [readr::write_tsv()] to do it efficiently.
#' 
#' @param file Output file (whatever is accepted by [readr::write_tsv()]).
#' If file is missing the expected *.snp extension, the function adds it.
#' @param tib The tibble or data.frame to write.
#' It must contain these columns: `id`, `chr`, `posg`, `pos`, `ref`, `alt`.
#' Throws an error if any of these columns are missing.
#' Additional columns are ignored.
#' Columns are automatically reordered in output as expected in format.
#' @param verbose If `TRUE` (default), function reports the path of the file being written (after autocompleting the extension).
#'
#' @return The output `tib` invisibly (what [readr::write_tsv()] returns).
#'
#' @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)
#' 
#' @seealso
#' Eigenstrat SNP format reference:
#' <https://github.com/DReichLab/EIG/tree/master/CONVERTF>
#'
#' @export
write_snp <- function(file, tib, verbose = TRUE) {
    # this generic writer does all the magic
    write_tab_generic(
        file = file,
        tib = tib,
        ext = 'snp',
        tib_names = snp_names,
        verbose = verbose
    )
}