Exploration of marker-gene sequence taxonomic annotations


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Documentation for package ‘metagenomeFeatures’ version 1.2.2

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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.
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
MgDb Metagenome Database class
mgdb Metagenome Database class
MgDb-class Metagenome Database class
mgdb_meta MgDb metadata slot accessor
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
msd16s_query_df Example Query Data Frame
select Querying MgDb objects
select-method Querying MgDb objects
show-method Display summary of MgDb-class object
taxa_columns Column names for MgDb taxonomy slot object
taxa_keys Taxonomy values for a given keytype
taxa_keytypes Column names for MgDb taxonomy slot object
taxa_levels Accessior function for taxanomic levels in MRexperiment featureData