paxtoolsr (version 1.6.3)

toGSEA: Converts a BioPAX OWL file to a GSEA GMT gene set

Description

This function converts pathway information stored as BioPAX files into the the GSEA .gmt format.

Usage

toGSEA(inputFile, outputFile = NULL, database, crossSpeciesCheckFlag)

Arguments

inputFile

a string of the name of the input OWL file

outputFile

a string of the name of the output file

database

a string of the name of the identifier type to be included (e.g. "HGNC Symbol")

crossSpeciesCheckFlag

a boolean that ensures participant protein is from same species

Value

• see readGmt()

concept

paxtoolsr

Details

The GSEA GMT format is a tab-delimited format where each row represents a gene set. The first column is the gene set name. The second column is a brief description. Other columns for each row contain genes in the gene set; these rows may be of unequal lengths.

Examples

outFile <- tempfile()
results <- toGSEA(system.file("extdata", "biopax3-short-metabolic-pathway.owl", 
                              package="paxtoolsr"), 
                              outFile, 
                              "uniprot", 
                              crossSpeciesCheckFlag=TRUE)