filter_orgs: Filter OTUs and kegg organisms

In tbradley1013/KEGGerator: Identify genomic functionality with KEGG

Description

Filter OTUs and kegg organisms

Usage

filter_orgs(data, uncertainty, pathway_name, pathways, verbose, progress)

## S3 method for class 'keggerator'
filter_orgs(data, uncertainty = 1,
  pathway_name = NULL, pathways = NULL, verbose = FALSE,
  progress = TRUE)

Arguments

data	a tibble that has genome_ids - likely the output from get_genome_id()
pathway_name	the name of the pathway that you wish to filter
pathways	a kegg_tbl dataset of available kegg pathways. This dataset is produced from the get_kegg_pathway function. If it is NULL (default) the KEGGerator::kegg_pathways dataset will be used

Methods (by class)

• keggerator: method for keggerator objects

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