dbReadLocus: Taxon-Locus-Crosstable

In heibl/megaptera: MEGAPhylogeny Techniques in R

Description

Create a data frame that contains for each taxon and locus the number of accessions found on GenBank/BOLD/etc. and if the taxon was selected for alignment.

Usage

dbReadLocus(megProj, provenance = ".", tag, subset)

Arguments

megProj	An object of class megapteraProj.
provenance	A characters string as used in the column provenance the acc_<locus> tables in the postgreSQL database. Depending on your actual pipeline setup these may be "ncbi", "ncbi annotated", or "bold" as well as any user-defined strings.
tag	Deprecated! A characters string as used in the column tag in the taxonomy table in the postgreSQL database. Depending on your choices for parameter values in taxon or taxonGuidetree these may be "ingroup (NCBI)", "extended ingroup (NCBI)", "outgroup (NCBI)", or "extended outgroup (NCBI)" as well as any user-defined strings.
subset	A vector of mode "character", that can be used to choose a subset of the total taxa available.

Value

A data frame with two types of colums

gb_<locus>	gives the number of accessions per taxon and locus
sel_<locus>	states if a taxon was selected for final alignment

See Also

checkSpecLocus

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