select-MgDb-method: Querying MgDb objects

Description Usage Arguments Value Examples

Description

Function for querying MgDb-class class objects, user defines the taxonomic levels (keytype) and a vector of taxonomic names (keys) being selected. If specific database ids are being selected for use keytype="Keys". Additionally, users can specify whether they want only the taxonomic and sequence data, or both.

Usage

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mgDb_select(mgdb, type, ...)

## S4 method for signature 'MgDb'
mgDb_select(mgdb, type, keys = NULL, keytype = NULL,
  columns = "all")

Arguments

mgdb

MgDb class object

type

either "taxa", "seq", "tree", "all" or a character vector of types. "taxa", "seq", and "tree" only query the reference taxonomy, sequences, and phylogenetic tree respectively. "all" queries the reference taxonomy, sequence, and phylogenetic tree.

...

additional arguments passed to select function

keys

specific taxonomic groups to select for

keytype

taxonomic level of keys

columns

keytypes in taxonomy databse to return, all by default

Value

returned object depends on type: 'taxa' - dataframe with taxa information; 'seq' - DNAStringSet with seqeunce data; 'tree' - phylogenetic tree of class phylo; 'all' - list with the dataframe, DNAStringSet, and phylo.

Examples

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gg85 <- get_gg13.8_85MgDb()
# select taxa only
mgDb_select(gg85, type = "taxa",
     keys = c("Vibrionaceae", "Enterobacteriaceae"),
     keytype = "Family")

# select seq only
 mgDb_select(gg85, type = "seq",
      keys = c("Vibrionaceae", "Enterobacteriaceae"),
      keytype = "Family")

# select all taxa, seq, and tree
mgDb_select(gg85, type = "all",
       keys = c("Vibrionaceae", "Enterobacteriaceae"),
       keytype = "Family")

metagenomeFeatures documentation built on Nov. 8, 2020, 5:18 p.m.