# Exploration of marker-gene sequence taxonomic annotations

## Documentation for package ‘metagenomeFeatures’ version 1.8.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

aggregate_taxa | Aggregates a MRexperiment object and returns either an aggregated MRexperiment or counts matrix to a user defined taxonomic level.
annotateFeatures | Annotating metagenome data with taxonomic information
annotateFeatures-method | Annotating metagenome data with taxonomic information
annotateMRexp_fData | Annotate MRexperiment object featureData slot using MgDb object
annotateMRexp_fData-method | Annotate MRexperiment object featureData slot using MgDb object
get_demoMgDb | Example MgDb-class object
get_mockMgDb | Mock MgDb-class object
MgDb | Metagenome Database class
mgdb | Metagenome Database class
MgDb-class | Metagenome Database class
mgdb_meta | MgDb metadata slot accessor
mgDb_select | Querying MgDb objects
mgDb_select-method | Querying MgDb objects
mgdb_seq | MgDb seq slot accessor
mgdb_taxa | MgDb taxa slot accessor
mgdb_tree | MgDb tree slot accessor
mgFeatures-class | mgFeature-class object
mgF_meta | mgFeatures metadata slot accessor
mgF_seq | mgFeatures refDbSeq slot accessor
mgF_taxa | mgFeatures taxa slot accessor
mgF_tree | mgFeatures refDbTree slot accessor
mgQuery | Example ShortRead 16S experiment dataset
mock_mgF | Example mgFeatures class object
mock_query_df | Example Query Data Frame
select-method | Querying MgDb objects
show-method | Display summary of MgDb-class object
taxa_columns | Column names for MgDb taxonomy slot object
taxa_columns-method | Column names for MgDb taxonomy slot object
taxa_keys | Taxonomy values for a given keytype
taxa_keys-method | Taxonomy values for a given keytype
taxa_keytypes | Column names for MgDb taxonomy slot object
taxa_keytypes-method | Column names for MgDb taxonomy slot object
taxa_levels | Accessor function for taxonomic levels in MRexperiment featureData