windows-specific-functions: Windows specific functions.

In topdownr: Investigation of Fragmentation Conditions in Top-Down Proteomics

Description

The functions runXmlMethodChanger and runScanHeadsman call XmlMethodChanger.exe and ScanHeadsman.exe with the corresponding arguments. The only work on Windows (maybe on Linux + wine as well but that was never tested).

Usage

createTngFusionMethFiles(
  template,
  xml = list.files(pattern = ".*\\.xml$"),
  executable = "XmlMethodChanger.exe",
  verbose = interactive()
)

runXmlMethodChanger(
  template,
  xml = list.files(pattern = ".*\\.xml$"),
  executable = "XmlMethodChanger.exe",
  verbose = interactive()
)

runScanHeadsman(path = ".", executable = "ScanHeadsman.exe")

Arguments

template	character, path to template .meth file.
xml	character, vector of path to .xml files.
executable	character, path to the XmlMethodChanger.exe or ScanHeadsman.exe executable.
verbose	logical, if TRUE a progress bar is shown.
path	character, path to the directory containing the .raw files.

Details

runXmlMethodChanger applies <e2><80><98>XmlMethodChanger.exe<e2><80><99> on all given XML files generated with writeMethodXmls() to create .meth files from a template.

runScanHeadsman calls ScanHeadsman.exe on a given directory containing .raw files. ScanHeadsman.exe extracts the method and scan header data into .experiments.csv and .txt files, respectively.

Value

Nothing. Used for its side effects.

References

XmlMethodChanger source code: https://github.com/thermofisherlsms/meth-modifications/

ScanHeadsman source code: https://bitbucket.org/caetera/scanheadsman

See Also

writeMethodXmls()

Examples

## Not run: 
runXmlMethodChanger(templateMeth="TMS2IndependentTemplate240Extended.meth",
                    modificationXml=list.files(pattern="^method.*\\.xml$"),
                    executable="..\\XmlMethodChanger.exe")

## End(Not run)
## Not run: 
runScanHeadsman("raw", executable="..\\ScanHeadsman.exe")

## End(Not run)

topdownr documentation built on Nov. 8, 2020, 8:10 p.m.