# Exploration of marker-gene sequence taxonomic annotations

## Documentation for package ‘metagenomeFeatures’ version 2.6.0

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

## Help Pages

annotateFeatures | Annotating metagenome data with taxonomic information
annotateFeatures-method | Annotating metagenome data with taxonomic information
get_gg13.8_85MgDb | MgDb-class object with Greengenes Database Version 13.8 85% OTUs
mgdb | Metagenome Database class
MgDb-accessor | MgDb-class accessors
MgDb-class | Metagenome Database class
MgDb-methods | Display summary of MgDb-class object
mgDb_meta | MgDb-class accessors
mgDb_select | Querying MgDb objects
mgDb_select-method | Querying MgDb objects
mgDb_seq | MgDb-class accessors
mgDb_taxa | MgDb-class accessors
mgDb_tree | MgDb-class accessors
mgFeatures | Class mgFeature
mgFeatures-accessors | mgFeatures accessors
mgFeatures-class | Class mgFeature
mgFeatures-methods | mgFeatures-class subset method
mgF_meta | mgFeatures accessors
mgF_seq | mgFeatures accessors
mgF_taxa | mgFeatures accessors
mgF_tree | mgFeatures accessors
mock_mgF | Example mgFeatures class object
mock_query_df | Example Query Data Frame
newMgDb | MgDb
qiita_study_94_gg_ids | QIITA Dataset For this vignette we are using 16S rRNA data from Rousk et al. 2010, a soil microbiome study, https://qiita.ucsd.edu/study/description/94. A BIOM and qiime mapping file for the study can be obtained from QIITA. A vector of Greengenes for the study cluster centers is included in this package for use in this vignette.
select-method | Querying MgDb objects
show-method | Display summary of MgDb-class object
taxa_ | MgDb-class Taxa slot helper functions
taxa_columns | MgDb-class Taxa slot helper functions
taxa_columns-method | MgDb-class Taxa slot helper functions
taxa_keys | MgDb-class Taxa slot helper functions
taxa_keys-method | MgDb-class Taxa slot helper functions
taxa_keytypes | MgDb-class Taxa slot helper functions
taxa_keytypes-method | MgDb-class Taxa slot helper functions
[-method | mgFeatures-class subset method