unify_biopax_ids: Uniformly Format IDs in BioPAX

In grishagin/RIGbiopax: Extract and Compare Genes and Pathways from BioPAX

Description

Converts IDs in a BioPAX object or a BioPAX-style data table to a uniform format.

Usage

unify_biopax_ids(biopax, idtag = NULL,
  exclude_id_pattern = "inxight_pathways", exclude_class = "Pathway")

Arguments

biopax	BioPAX object or a BioPAX-style data table.
idtag	String to append to each id (defaults to NULL).
exclude_id_pattern	Exclude components with such pattern in their IDs and of class exclude_class from ID unification.
exclude_class	Exclude components with such class and exclude_id_pattern from ID unification.

Details

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". In addition, component classes are corrected as well to ensure that components with the same id have the same class.

Author(s)

Ivan Grishagin

grishagin/RIGbiopax documentation built on May 24, 2019, 1:33 a.m.