MAIN_compare_toxdb_biopax: Compare Proteins Extracted from BioPAX to ToxDB Proteins
In grishagin/RIGbiopax: Extract and Compare Genes and Pathways from BioPAX

Description Usage Arguments Author(s)

Main function of the package. Extract all proteins ("genes") from a BioPAX source, convert their IDs to gene IDs and Symbols, and then compare those to a supplied gene list.

MAIN_compare_toxdb_biopax(work_dir = NULL, source_owl_dir = NULL,
  output_dir = NULL, pw_matchup_file = "default",
  toxdb_genes_file = "default", source_name = NULL,
  owl_biopax = NULL, verbose = FALSE)

`work_dir`	Directory, where all source files/folders are located and will be written to.
`source_owl_dir`	Directory with `*.owl` files. If no directory provided, a prompt will pop up. See `load_biopax` function for more information.
`output_dir`	.
`pw_matchup_file`	File that provides match-up between inxight pathway names and BioPAX pathway names.
`toxdb_genes_file`	File that has a table of all genes listed for all pathways.
`source_name`	Name of the BioPAX source.
`owl_biopax`	BioPAX object.
`verbose`	Logical. Show all relevant progress messages?