validate: 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)

Value

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

concept

paxtoolsr

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.

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)