gene_bag_to_biopax: Convert a "Gene Bag" Data Table to BioPAX Object

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

Description

Converts a data table with pathway and gene IDs (a "gene bag") to a BioPAX object. Has an option of recording the BioPAX object to file.

Usage

gene_bag_to_biopax(gene_df
                   ,filename=NULL
                   ,cols=list(pwid="Pathway.ID"
                        ,pwname="Pathway.Name"
                        ,genedisplayname="Gene.Symbol"
                        ,genename="Gene.Name"
                        ,genesymbol="Gene.Symbol"
                        ,geneid="Gene.ID")
                   )

Arguments

gene_df	data table with mandatory columns: Pathway.Name, Pathway.ID, Gene.Symbol, Gene.ID.
filename	output filename. If NULL (default), does not output to file.
cols	gene_df columns, assigned to self-explanatory variables used within the function.

Author(s)

Ivan Grishagin

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