validate {paxtoolsr} | R Documentation

## Validate BioPAX files

### Description

This function validates BioPAX files for errors.

### Usage

    validate(
      inputFile,
      outputFile = NULL,
      type = c("xml", "html", "biopax"),
      autoFix = FALSE,
      onlyErrors = FALSE,
      maxErrors = NULL,
      notStrict = FALSE
    )

### Arguments

`inputFile` | a string of the name of the input BioPAX OWL file
`outputFile` | a string of the name of the output file containing validation results
`type` | a string denoting the type of output: xml (default), html, biopax
`autoFix` | a boolean that determines if the input file should be fixed automatically. Errors that can be automatically fixed include generating displayName properties from names, inferring organism, and inferring dataSource
`onlyErrors` | a boolean of whether to only display errors
`maxErrors` | a integer denoting the number of errors to return
`notStrict` | a boolean of whether to be strict in validation (default: FALSE)

### Details

See the publication by Rodchenkov, et al. for information on the BioPAX validator. See http://biopax.baderlab.org/validator for additional information on validator. See http://biopax.baderlab.org/validator/errorTypes.html for information on error types.

### Value

an XMLInternalDocument is returned if type is set to "xml" otherwise the location of the outputfile is returned.

### References

Rodchenkov I, Demir E, Sander C, Bader GD. The BioPAX Validator, http://www.ncbi.nlm.nih.gov/pubmed/23918249

### Examples

    outFile <- tempfile()
    rawDoc <- validate(system.file("extdata", "raf_map_kinase_cascade_reactome.owl",
      package="paxtoolsr"), onlyErrors=TRUE)

[Package paxtoolsr version 1.26.0 Index]