validatePSIMI25 {RpsiXML} | R Documentation |
The function validates given PSI-MI 2.5 file with MIF25 XML schema provided by the Molecular Interactions Workgroup of HUPO Proteomics Standards Initiative
validatePSIMI25(file, schema = system.file("extdata/schemas/MIF25.xsd", package = "RpsiXML"), ignore.stderr = TRUE)
file |
The name or the URL of the file to be validated |
schema |
The schema file of PSI-MI 2.5 file format by default |
ignore.stderr |
Whether to print out errors in the console |
We advice to set "ignore.stderr=FALSE" for the first time of validating. The error number of the file will be printed in the console. When the number is not 0, one can set "ignore.stderr=TRUE" and see the errors produced during the validation.
The number of errors in validating the file
This function sofar depends on the tool "xmllint" bundled with libxml2 library. We plan to compile it later to run independent of the tool.
Jitao David Zhang <j.zhang@dkfz.de>, Tony Chiang <tchiang@ebi.ac.uk>
libxml2 library http://xmlsoft.org/ PSI-MI 2.5 XML schema http://psidev.sourceforge.net/mi/rel25/src/MIF25.xsd
okFile <- system.file("extdata/psi25files/intact_2008_test.xml", package="RpsiXML") validatePSIMI25(okFile)