genes_and_interactions_to_biopax: Convert a Data Table with Genes and Interactions to BioPAX...
In grishagin/RIGbiopax: Extract and Compare Genes and Pathways from BioPAX

Description Usage Arguments Details Author(s)

Converts a data table with pathway and gene IDs and interactions between them to a BioPAX object.

genes_and_interactions_to_biopax(gene_df
                               ,filename = NULL
                               ,cols = list(pwid = "toxdb.Pathway.ID"
                                        ,srcpwname = "source.Pathway.Name"
                                        ,first_dispname = "first_prot_sym"
                                        ,first_name = "first_name"
                                        ,first_genesym = "first_gene_sym"
                                        ,first_geneid = "first_gene_id"
                                        ,second_dispname = "second_prot_sym"	
                                        ,second_name = "second_name"
                                        ,second_genesym = "second_gene_sym"
                                        ,second_geneid = "second_gene_id"
                                        ,pmid_author = "pmid_author"
                                        ,rxn_class = "reaction_class"
                                        ,ctrl_class = "control_class"
                                        ,ctrl_type = "control_type"
                                        ,second_left_right = "second_left_right"
                                        )

`gene_df`	data table with certain mandatory columns (see `cols` argument). Briefly, takes in a table with first and second gene parameters (gene ids, names, etc.) and reaction information (control class and type, reaction class, etc.).
`filename`	output filename. If `NULL` (default), does not output to file.
`cols`	`gene_df` columns assigned to self-explanatory variables used within the function.