taxa_: MgDb-class Taxa slot helper functions

In metagenomeFeatures: Exploration of marker-gene sequence taxonomic annotations

Description

Helper functions for for MgDb-class taxa slot. taxa_columns - taxa slot column names, taxa_keytypes - taxa slot keytypes (values used with taxa_columns and mgDb_select functions), and taxa_keys - database values for a specific keytype.

Usage

taxa_keys(mgdb, keytype)

## S4 method for signature 'MgDb'
taxa_keys(mgdb, keytype)

taxa_columns(mgdb)

## S4 method for signature 'MgDb'
taxa_columns(mgdb)

taxa_keytypes(mgdb)

## S4 method for signature 'MgDb'
taxa_keytypes(mgdb)

Arguments

mgdb	MgDb-class object.
keytype	character string specifying keys to return

Value

appropriate class object for the slot accessed

Examples

gg85 <- get_gg13.8_85MgDb()
taxa_columns(gg85)
taxa_keytypes(gg85)
taxa_keys(gg85, keytype = "Phylum")

metagenomeFeatures documentation built on Nov. 8, 2020, 5:18 p.m.