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

In alyst/RpsiXML: R interface to PSI-MI 2.5 files

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 <[e-mail]>, Tony Chiang <[e-mail]>

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)

alyst/RpsiXML documentation built on Nov. 21, 2019, 5:47 a.m.