megapteraProj-class: Class "megapteraProj"

In heibl/megaptera: MEGAPhylogeny Techniques in R

Description

S4 class for holding all input data of the megaptera pipeline.

Slots

db

An object of class dbPars.

taxon

An object of classes taxon or taxonGuidetree.

locus

An object of classes locus or locusRef.

align.exe

A vector of mode "character", giving name of the alignment program; currently only MAFFT is allowed.

merge.exe

A vector of mode "character", giving name of the alignment merging program; currently only OPAL is allowed.

mask.exe

A vector of mode "character", giving name of the alignment masking program; currently only Gblocks is allowed.

params

An object of class megapteraPars.

update

Logical: if TRUE, the pipeline's steps are executed as if called for the first time, i.e., possibly overriding data and setting that have been previously achieved.

See Also

dbPars, taxon, locus, and megapteraPars for defining of database parameters, taxa, loci, and the pipeline's parameters, respectively.

heibl/megaptera documentation built on Jan. 17, 2021, 3:34 a.m.