megapteraProj-class


Class for holding all input data of the pipeline.


Given a set of taxa and marker, the goal is build a complete and correct sequence alignment for phylogenetic analysis.

Christoph Heibl

megaptera

MEGAPhylogeny Techniques in R

megapteraProj-class function

Objects can be created by calls of the form <code>megapteraProj(db, taxon, locus, align.exe, mask.exe, params = megapteraPars(), update = FALSE, parallel = FALSE)</code>.

Objects from the Class

<dl>
  <dt>db</dt><dd>an object of class <code><a rd-options="" href="/link/dbPars?package=megaptera&version=1.0-0" data-mini-rdoc="megaptera::dbPars">dbPars</a></code>.</dd> <dt>taxon</dt><dd>an object of class <code><a rd-options="" href="/link/taxon?package=megaptera&version=1.0-0" data-mini-rdoc="megaptera::taxon">taxon</a></code>.</dd> <dt>locus</dt><dd>an object of class <code><a rd-options="" href="/link/locus?package=megaptera&version=1.0-0" data-mini-rdoc="megaptera::locus">locus</a></code>.</dd> <dt>align.exe</dt><dd>
a vector of mode <code>"character"</code>, giving name of the alignment program; currently only <b>MAFFT</b> is allowed
</dd> <dt>mask.exe</dt><dd>
a vector of mode <code>"character"</code>, giving name of the alignment masking program; currently only <b>Gblocks</b> is allowed
</dd> <dt>params</dt><dd>an object of class <code><a rd-options="" href="/link/megapteraPars?package=megaptera&version=1.0-0" data-mini-rdoc="megaptera::megapteraPars">megapteraPars</a></code>.</dd> <dt>update</dt><dd>
logical: if <code>TRUE</code>, the pipeline's steps are executed as if called fro the first time, i.e., possibly overriding data and setting that have been previously achieved.
</dd> <dt>parallel</dt><dd>
logical: if <code>TRUE</code>, several step in the pipeline will be run in parallel, otherwise all steps are serial.
  </dd> </dl> 

megapteraProj-class: Class "megapteraProj"

Description

Arguments

Objects from the Class

Slots

See Also