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.
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/23918249Examples
outFile <- tempfile()
rawDoc <- validate(system.file("extdata", "raf_map_kinase_cascade_reactome.owl",
package="paxtoolsr"), onlyErrors=TRUE)