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

Description Usage Arguments Details Methods (by class)

Query all orthologies related to each genome in the dataset

get_orthologies(data, pathway_orthologies, kegg_orthology, verbose,
  progress)

## S3 method for class 'keggerator'
get_orthologies(data, pathway_orthologies = NULL,
  kegg_orthology = NULL, verbose = FALSE, progress = TRUE)

## S3 method for class 'orgs_id'
get_orthologies(orgs_id, pathway_orthologies = NULL,
  kegg_orthology = NULL, verbose = FALSE, progress = TRUE)

`data`	a tibble with genomes and genome_id or the output from 'get_genome_id()'
`pathway_orthologies`	a vector of pathway orthologies
`kegg_orthology`	a kegg_tbl with the columns orthology and orthology_id which can be generated with the get_kegg_orthology function. If NULL (default) the KEGGerator::kegg_orthologies 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_orthologies' is NULL (default) than all orthologies for each genome will be returned. If a vector of orthology_ids is provided than only the orthologies 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_orthologies' to only include the orthologies 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.