get_enzymes: Query all enzymes related to each genome in the dataset
In tbradley1013/KEGGerator: Identify genomic functionality with KEGG

Description Usage Arguments Details Methods (by class)

Query all enzymes related to each genome in the dataset

get_enzymes(data, pathway_enzymes, kegg_enzymes, verbose, progress)

## S3 method for class 'keggerator'
get_enzymes(data, pathway_enzymes = NULL,
  kegg_enzymes = NULL, verbose = FALSE, progress = TRUE)

## S3 method for class 'orgs_id'
get_enzymes(orgs_id, pathway_enzymes = NULL,
  kegg_enzymes = NULL, verbose = FALSE, progress = TRUE)

`data`	a tibble with genomes and genome_id or the output from 'get_genome_id()'
`pathway_enzymes`	a vector of pathway enzymes
`kegg_enzymes`	a kegg_tbl that has the columns enzyme and enzyme_id. This can be generated using the get_kegg_enzyme() function. If NULL (default) than the KEGGerator::kegg_enzymes dataset will be used
`verbose`	logical; if TRUE the number of enzyme links for each genome id will be shown as they are processed
`progress`	logical; if TRUE (default) than a progress bar will appear if the query takes longer than 10 seconds (it likely will if your data has more) than only a few genomes

if 'pathway_enzymes' is NULL (default) than all enzymes for each genome will be returned. If a vector of enzyme_ids is provided than only the enzymes related to each genome that are in this vector will be returned. This is useful if used in coordination with the output of 'get_pathway_enzymes' to only include the enzymes that are related with the pathway of interest.

keggerator: method for keggerator objects
orgs_id: method for orgs_id objects

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