MAIN_combine_clean_biopax_unifyids: MAIN - Combine and Clean List of BioPAX Objects

In grishagin/RIGconvertbiopax: Convert BioPAX into Flat File and Back

Description

Merges BioPAX objects, unifies component IDs, replaces certain pathway ids with proper inxight_pathway ones, and cleans BioPAX objects from html tags and garbled symbols.

Usage

MAIN_combine_clean_biopax_unifyids(new_biopax_list, pw_df_path = "default",
  exclude_id_pattern = "inxight_pathways")

Arguments

new_biopax_list	List of BioPAX objects.
pw_df_path	Path to the source table with pathway, id, name, and source values.
exclude_id_pattern	Exclude pathways with such pattern in their IDs from ID unification.

Details

Wrapper for unify_biopax_ids and biopax_from_dt. ID unification is conducted by appending a class of a component to its throughout number. E.g. for a component of class Protein, #11 from the top of the table, ID will be "Protein11".

Author(s)

Ivan Grishagin

grishagin/RIGconvertbiopax documentation built on May 5, 2019, 9:18 a.m.