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Download OMIM Files

download_omim.Rd

Downloads one or more specified files from OMIM (the Online catalog of Mendelian Inheritance in Man). mim2gene.txt is the only file accessible without an API key from OMIM.

Usage

download_omim(omim_file, dest_dir, api_key = NULL, on_failure = "abort", ...)

Arguments

omim_file

A character vector of one or more OMIM file name(s).

dest_dir

Path to directory where files will be saved; all OMIM files are saved in .txt format and consist of tab-separated values with a copyright header.

api_key

Your API key from OMIM, as a string; required if downloading any file other than 'mim2gene.txt'.

Register for downloads at OMIM.

on_failure

A string indicating how to handle download failure:

  • "warn" - produce a warning; includes exit codes for debugging

  • "abort" - abort execution

  • "list_failed" - list URLs that failed (output format differs, see Value)

  • "warn-list_failed" - combination of "warn" and "list_failed"

  • "skip" - do nothing

...

Additional arguments passed on to utils::download.file().

Value

Unless on_failure includes "list_failed", the successfully downloaded dest_file(s); otherwise, a 2-vector list where successful = dest_file(s) and failed = url(s).

See also

read_omim() to read downloaded files as tibble/data.frames.