select-MgDb-method: Querying MgDb objects

In HCBravoLab/metagenomeFeatures: Exploration of marker-gene sequence taxonomic annotations

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

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

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")

HCBravoLab/metagenomeFeatures documentation built on Feb. 14, 2020, 12:42 a.m.