utils.plink.run

Facilitates the import and analysis of 'SNP' (single nucleotide 'polymorphism')
and 'silicodart' (presence/absence) data. The main focus is on data generated by 'DarT'
(Diversity Arrays Technology), however, data from other sequencing platforms can be used
once 'SNP' or related fragment presence/absence data from any source is imported. Genetic
datasets are stored in a derived 'genlight' format (package 'adegenet'), that allows for
a very compact storage of data and metadata. Functions are available for
importing and exporting of 'SNP' and 'silicodart' data, for reporting on and
filtering on various criteria (e.g. 'callrate', 'heterozygosity', 'reproducibility',
maximum allele frequency). Additional functions are available for visualization
(e.g. Principle Coordinate Analysis) and creating a spatial representation
using maps. 'dartR.base' is the 'base' package of the 'dartRverse' suits of packages.
To install the other packages, we recommend to install the 'dartRverse' package, that
supports the installation of all packages in the 'dartRverse'.
If you want to cite 'dartR', you find the information by typing citation('dartR.base')
in the console.

Bernd Gruber

dartR.base

Analysing 'SNP' and 'Silicodart' Data - Basic Functions

Arthur Georges

Jose L. Mijangos

Carlo Pacioni

Diana Robledo-Ruiz

Peter J. Unmack

Oliver Berry

Lindsay V. Clark

Floriaan Devloo-Delva

Eric Archer

Ching Ching Lau

utils.plink.run function

<dl><dt>dir.in</dt>
<dd>The path where the data files are</dd>
<dt>plink.cmd</dt>
<dd>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</dd>
<dt>plink.path</dt>
<dd>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</dd>
<dt>out</dt>
<dd>The root of the output file name</dd>
<dt>syntax</dt>
<dd>the flags to pass to plink call</dd>
<dt>verbose</dt>
<dd>Verbosity: 0, silent or fatal errors; 1, begin and end; 2,
progress log; 3, progress and results summary; 5, full report [default NULL].</dd></dl>

Arguments

Custodian: Carlo Pacioni and Luis Mijangos (Post to
 <a href="https://groups.google.com/d/forum/dartr">https://groups.google.com/d/forum/dartr</a>)

Author

Runs PLINK from within R — utils.plink.run

<dl>

<dt>dir.in</dt>
<dd>The path where the data files are</dd>


<dt>plink.cmd</dt>
<dd>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</dd>


<dt>plink.path</dt>
<dd>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</dd>


<dt>out</dt>
<dd>The root of the output file name</dd>


<dt>syntax</dt>
<dd>the flags to pass to plink call</dd>


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

</dl>

Custodian: Carlo Pacioni and Luis Mijangos (Post to
 <a href='https://groups.google.com/d/forum/dartr'>https://groups.google.com/d/forum/dartr</a>)

utils.plink.run: Runs PLINK from within R

Description

Usage

Value

Arguments

Author

Details

References