load_pangenomeRDS

This function loads a pagoo pangenome from a `.RDS` file generated
by the `save_pangenomeRDS` method. Objects loaded by this functions keep their
states, i.e : dropped/recovered organisms are conserved, as well as the
`core_level` setted when the object was originally saved.

Provides an encapsulated, object-oriented class system for
analyzing bacterial pangenomes. For a definition of this concept, see
Tettelin, et al. (2005) <doi:10.1073/pnas.0506758102>. It uses the R6
package as backend. It was designed in order to facilitate and speed-up
the comparative analysis of multiple bacterial genomes, standardizing and
optimizing routine tasks performed everyday. There are a handful of things
done everyday when working with bacterial pangenomes: subset, summarize,
extract, visualize and store data. So, 'pagoo' is intended to facilitate these
tasks as much as possible. For a description of the implemented data structure
and methods, see Ferres & Iraola (2020), <doi:10.1101/2020.07.29.226951>.

Ignacio Ferres

pagoo

Analyze Bacterial Pangenomes in R with 'Pagoo'

Gregorio Iraola

Institut Pasteur de Montevideo 

load_pangenomeRDS function

<dl><dt>file</dt>
<dd>The path to the pangenome `.RDS` file.</dd>
<dt>pkg</dt>
<dd>The package to use to load the object. Shouldn't be necessary to
provide, but may be useful in some cases.</dd>
<dt>...</dt>
<dd>Arguments to be passed to the pagoo object. <code>sep</code> and
<code>core_level</code> overwrite the values stored in the file.</dd></dl>

Arguments

Load A Pagoo Pangenome — load_pangenomeRDS

<dl>

<dt>file</dt>
<dd>The path to the pangenome `.RDS` file.</dd>


<dt>pkg</dt>
<dd>The package to use to load the object. Shouldn't be necessary to
provide, but may be useful in some cases.</dd>


<dt>...</dt>
<dd>Arguments to be passed to the pagoo object. <code>sep</code> and
<code>core_level</code> overwrite the values stored in the file.</dd>

</dl>

load_pangenomeRDS: Load A Pagoo Pangenome

Description

Usage

Value

Arguments