megapteraProj-class: Class "megapteraProj"

In megaptera: MEGAPhylogeny Techniques in R

Description

Class for holding all input data of the pipeline.

Objects from the Class

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

Slots

db

an object of class dbPars.

taxon

an object of class taxon.

locus

an object of class locus.

align.exe

a vector of mode "character", giving name of the alignment program; currently only MAFFT 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 fro the first time, i.e., possibly overriding data and setting that have been previously achieved.

parallel

logical: if TRUE, several step in the pipeline will be run in parallel, otherwise all steps are serial.

Author(s)

Christoph Heibl

See Also

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

megaptera documentation built on Jan. 15, 2017, 11:19 p.m.