dbManipulateSpec: Manipulate Single Species in Database
In heibl/megaptera: MEGAPhylogeny Techniques in R

Description Usage Arguments Value Note Author(s) See Also

Manually manipulate problematic species that are not handled satisfactorily by the parameters identity and coverage: delete a species from the PostgreSQL database, exclude a species from alignment, or include (a formerly excluded) species in alignment.

dbDeleteSpec(x, spec)

dbExcludeSpec(x, spec)

dbIncludeSpec(x, spec)

`x`	an object of class `megapteraProj`.
`spec`	a character string giving a species name.

None; as a side effect the table "locus" and "spec_<gene>" are updated.

dbExcludeSpec must be called between stepF and stepMAFFT. Because stepF rewrites the spec_<locus> table, dbExcludeSpec must be called again after every use of stepF. Note that there is no warning if manual exclusions set with dbExcludeSpec are eliminated by stepF.

Christoph Heibl

dbUpdateTaxonomy, dbReadTaxonomy, dbWriteDNA, dbReadDNA

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