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

In paxtoolsr: PaxtoolsR: Access Pathways from Multiple Databases through BioPAX and Pathway Commons

Description

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

Usage

toGSEA(
  inputFile,
  outputFile = NULL,
  database = "uniprot",
  crossSpeciesCheckFlag = TRUE
)

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

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.

Value

see readGmt()

Examples

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

paxtoolsr documentation built on Nov. 8, 2020, 8:29 p.m.