RpsiXML (version 2.12.0)

validatePSIMI25: Validating PSI-MI 2.5 file with MIF25 XML schema

Description

The function validates given PSI-MI 2.5 file with MIF25 XML schema provided by the Molecular Interactions Workgroup of HUPO Proteomics Standards Initiative

Usage

validatePSIMI25(file, schema = system.file("extdata/schemas/MIF25.xsd", package = "RpsiXML"), ignore.stderr = TRUE)

Arguments

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

Value

The number of errors in validating the file

Details

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.

References

libxml2 library http://xmlsoft.org/ PSI-MI 2.5 XML schema http://psidev.sourceforge.net/mi/rel25/src/MIF25.xsd

Examples

Run this code
okFile <- system.file("extdata/psi25files/intact_2008_test.xml",
                      package="RpsiXML")
validatePSIMI25(okFile)

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