utils.plink.run {dartR.base}

Runs PLINK from within R

Description

Runs PLINK from within R.

Usage

utils.plink.run(
  dir.in,
  plink.cmd = "plink",
  plink.path = "path",
  out = "hapmap1",
  syntax,
  verbose = NULL
)

Arguments

dir.in

The path where the data files are

plink.cmd

The 'name' to call plink. This will depend on the file name (without the extension '.exe' if on windows) or the name of the PATH variable

plink.path

The path where the executable is. If plink is listed in the PATH then there is no need for this. This is what the option "path" means

out

The root of the output file name

syntax

the flags to pass to plink call

verbose

Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default NULL].

Details

PLINK needs to be installed on the machine and syntax used need to be appropriate for the version installed.

Value

A character vector with the command used for PLINK.

Author(s)

Custodian: Carlo Pacioni and Luis Mijangos (Post to https://groups.google.com/d/forum/dartr)

References

Purcell, Shaun, et al. 'PLINK: a tool set for whole-genome association and population-based linkage analyses.' The American journal of human genetics 81.3 (2007): 559-575.