MgDb-class: Metagenome Database class

In metagenomeFeatures: Exploration of marker-gene sequence taxonomic annotations

Description

The MgDb-class object contains sequence, taxonomic data, and a phylogenetic tree (optional) for a 16S rRNA taxonomic database, see the greengenes13.5MgDb package as an example database. The get_gg13.8_85MgDb() function in metagenomeFeatures exports a small subset of the database in the greengenes13.5MgDb annotation package as an example MgDb-class object.

Value

MgDb-class object

Slots

seq

database reference sequences

tree

reference phylogenetic tree

taxa

database taxonomy

metadata

associated metadata for the database

Note

Currently the only database with a MgDb package is the Greengenes database (version 13.5), additional packages are planned.

Examples

# example MgDb-class object, Greengenes 13.8 85% OTUs database.
gg85 <- get_gg13.8_85MgDb()

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