gl.read.PLINK {dartR.base}

Reads PLINK data file into a genlight object

Description

This function imports PLINK data into a genlight object and append available metadata.

Usage

gl.read.PLINK(
  filename,
  ind.metafile = NULL,
  loc.metafile = NULL,
  plink.cmd = "plink",
  plink.path = "path",
  plink.flags = NULL,
  verbose = NULL
)

Arguments

filename

Fully qualified path to PLINK input file (without including the extension)

ind.metafile

Name of the csv file containing the metrics for individuals [optional].

loc.metafile

Name of the csv file containing the metrics for loci [optional].

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

plink.flags

additional possible parameters passed on to plink.

verbose

Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default 2 or as specified using gl.set.verbosity].

Details

This function handles .ped or .bed file (with the associate files - e.g. .fam, .bim). However, if a .ped file is provided, PLINK needs to be installed and it is used to convert the .ped into a .bed, which is then converted into a genlight.

Additional metadata can be included passing .csv files. These will be appended to the existing metadata present in the PLINK files.

The locus metadata needs to be in a csv file with headings, with a mandatory column headed AlleleID corresponding exactly to the locus identity labels provided with the SNP data

Value

A genlight object with the SNP data and associated metadata included.

Author(s)

Custodian: Carlo Pacioni – Post to https://groups.google.com/d/forum/dartr