toGSEA {paxtoolsr} | R Documentation

## 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 = "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)

[Package paxtoolsr version 1.28.0 Index]