orgs_tibble: extract organisms from tax table or tax tibble

In tbradley1013/KEGGerator: Identify genomic functionality with KEGG

Description

extract organisms from tax table or tax tibble

Usage

orgs_tibble(data, drop_taxa, strict, sep)

## S3 method for class 'tax_tbl'
orgs_tibble(data, drop_taxa = TRUE, strict = FALSE,
  sep = "\\/")

## S3 method for class 'keggerator'
orgs_tibble(data, drop_taxa = TRUE,
  strict = FALSE, sep = "\\/")

## S3 method for class 'phyloseq'
orgs_tibble(data, drop_taxa = TRUE, strict = FALSE,
  sep = "\\/")

Arguments

data	either a phyloseq object or the output of tibble_tax
drop_taxa	logical; should the taxonomy be removed from the output
strict	logical; if set to TRUE, it will not keep any taxa that have not been classified to the species level.
sep	what is used to separate multiple species in the species column. Must be valid regex targeting the seperator. Default is "\/" to match the default separator used during taxonomic classification by addSpecies

Details

When an object of class tax_tbl is passed to orgs_tibble, a list with two tibbles will be returned. The first tibble is the orgs tibble and the second is the uncertainty tibble which is comprised of the percent uncertainty [0-1] of the species level assignment of each otu. If the otu was not assigned to the species level than the uncertainty level is 1. If the otu was assigned to only a single species than the uncertainty level is 0. If the species level was assigned to N possible species, than the uncertainty level is 1-(1/N).

If an object of class keggerator is passed to orgs_tibble than the same two tbls are returned, but rather than being in a list alone, they are added to the keggerator object that is given in the orgs_tbl and species_uncert slots, respectively.

Methods (by class)

• tax_tbl: method for tax_tbl

• keggerator: method for keggerator

• phyloseq: method for phyloseq object

tbradley1013/KEGGerator documentation built on Feb. 23, 2020, 6:44 a.m.