Exploration of marker-gene sequence taxonomic annotations

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Documentation for package ‘metagenomeFeatures’ version 2.8.0

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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