lcms_raw_to_mzxml: Raw to mzxml

In sipss/AlpsLCMS: Signal processing of LC-MS metabolomics

Description

Convert RAW samples to mzxml samples.

Usage

lcms_raw_to_mzxml(
  samples,
  options = c("--mzxml", "--select_mono_prec"),
  rawconverter = NULL
)

Arguments

samples	ThermoFisher .raw files.
options	Optios for the conversion.
rawconverter	The working directory given to install_RawConverter.

RawConverter

Raw samples from ThermoFisher are not easily parsed. All implementations go through the proprietary dll from Thermo.

This function uses a tool named RawConverter available at: http://fields.scripps.edu/rawconv/

RawConverter uses the ThermoFisher tool MSFileReader that takes care of the decryption.

Installing that tool may not be straightforward on all OS, so some helpers are provided to the user.

On non-Windows systems: You will need wine and winetricks installed. Then call install_RawConverter("/your/installation/directory")

sipss/AlpsLCMS documentation built on May 13, 2021, 6:18 p.m.