utils.read.fasta

WARNING: UTILITY SCRIPTS ARE FOR INTERNAL USE ONLY AND SHOULD NOT BE USED BY END USERS AS THEIR USE OUT OF CONTEXT COULD LEAD TO UNPREDICTABLE OUTCOMES.

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.read.fasta function

<dl><dt>file</dt>
<dd>Name of the fastA file [required]</dd>
<dt>parallel</dt>
<dd>Switch to deactivate parallel version. It might not be worth
to run it parallel most of the times [default FALSE]</dd>
<dt>n.cores</dt>
<dd>Number of cores to use in parallel [default 4]</dd>
<dt>verbose</dt>
<dd>Verbosity: 0, silent, fatal errors only; 1, flag function
begin and end; 2, progress log; 3, progress and results summary; 5, full
report [default 2 or as specified using gl.set.verbosity].</dd></dl>

Arguments

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

Author

An internal script to read a fastA file into a genlight object — utils.read.fasta

<dl>

<dt>file</dt>
<dd>Name of the fastA file [required]</dd>


<dt>parallel</dt>
<dd>Switch to deactivate parallel version. It might not be worth
to run it parallel most of the times [default FALSE]</dd>


<dt>n.cores</dt>
<dd>Number of cores to use in parallel [default 4]</dd>


<dt>verbose</dt>
<dd>Verbosity: 0, silent, fatal errors only; 1, flag function
begin and end; 2, progress log; 3, progress and results summary; 5, full
report [default 2 or as specified using gl.set.verbosity].</dd>

</dl>

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

utils.read.fasta: An internal script to read a fastA file into a genlight object

Description

Usage

Value

Arguments

Author

See Also