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 |