require_files_plink: Require that Plink binary files are present

In genio: Genetics Input/Output Functions

Require that Plink binary files are present

Description

This function checks that each of the Plink binary files (BED/BIM/FAM extensions) are present, given the shared base file path, stopping with an informative message if any of the files is missing. This function aids troubleshooting, as various downstream external software report missing files differently and sometimes using confusing or obscure messages.

Usage

require_files_plink(file)

Arguments

file	The shared file path (excluding extensions bed, bim, fam).

Value

Nothing

Examples

# to require all of "data.bed", "data.bim", and "data.fam", run like this:
# (stops if any of the three files is missing)
# require_files_plink("data")

# The following example is more awkward
# because package sample data has to be specified in this weird way:

# check that the samples we want exist
# start with bed file
file <- system.file("extdata", 'sample.bed', package = "genio", mustWork = TRUE)
# remove extension
file <- sub('\\.bed$', '', file)
# since all sample.{bed,bim,fam} files exist, this will not stop with error messages:
require_files_plink(file)

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