validatePSIMI25 {RpsiXML} | R Documentation

## 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

### 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.

### Value

The number of errors in validating the file

### Note

This function sofar depends on the tool "xmllint" bundled with libxml2 library. We plan to compile it later to run independent of the tool.

### Author(s)

Jitao David Zhang <jitao_david.zhang@roche.com>, Tony Chiang <tchiang@ebi.ac.uk>

### References

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

### Examples

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

[Package RpsiXML version 2.26.0 Index]