Exploration of marker-gene sequence taxonomic annotations


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Documentation for package ‘metagenomeFeatures’ version 1.10.0

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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