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metagenomeFeatures (version 1.2.2)

Exploration of marker-gene sequence taxonomic annotations

Description

metagenomeFeatures was developed for use in exploring the taxonomic annotations for a marker-gene metagenomic sequence dataset. The package can be used to explore the taxonomic composition of a marker-gene database or annotated sequences from a marker-gene metagenome experiment.

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Version

Version

1.2.2

License

Artistic-2.0

Issues

11

Pull Requests

0

Stars

10

Forks

5

Maintainer

Nathan D Olson

Last Published

February 15th, 2017

Functions in metagenomeFeatures (1.2.2)

mgdb_seq

MgDb seq slot accessor
mgdb_taxa

MgDb taxa slot accessor
taxa_levels

Accessior function for taxanomic levels in MRexperiment featureData
show,MgDb-method

Display summary of MgDb-class object
mgFeatures-class

mgFeature-class object
mgF_seq

mgFeatures refDbSeq slot accessor
mgF_tree

mgFeatures refDbTree slot accessor
aggregate_taxa

Aggregates a MRexperiment object and returns either an aggregated MRexperiment or counts matrix to a user defined taxonomic level.
select

Querying MgDb objects
annotateMRexp_fData

Annotate MRexperiment object featureData slot using MgDb object
MgDb-class

Metagenome Database class
mgF_meta

mgFeatures metadata slot accessor
mgdb_tree

MgDb tree slot accessor
taxa_columns

Column names for MgDb taxonomy slot object
mgF_taxa

mgFeatures taxa slot accessor
get_demoMgDb

Example MgDb-class object
mgdb_meta

MgDb metadata slot accessor
mgQuery

Example ShortRead 16S experiment dataset
msd16s_query_df

Example Query Data Frame
taxa_keytypes

Column names for MgDb taxonomy slot object
taxa_keys

Taxonomy values for a given keytype