rawFileConvert: Convert proprietory instrument manufacturer file types to...

In WMBEdmands/simExTargId: Simultaneous peak-picking and MS2 target identification using XCMS.

Description

Convert proprietory instrument manufacturer file types to .mzXML files

Usage

rawFileConvert(rawFiles = NULL, mzXmlDir = NULL, nCores = NULL,
  subSetSecs = NULL, zlib = TRUE, centroid = TRUE, MS2 = FALSE)

Arguments

rawFiles	character vector of full path names to raw data files.
mzXmlDir	character full path to directory into which to write the mzXml files output by MSConvert.
nCores	numeric number of computer cores for parallel computation.
subSetSecs	numeric vector of a minimum and maximum time window in mzXML files (e.g. c(1500, 1900)).
zlib	logical whether or not to apply zlib compression (default = TRUE). Will reduce file size but may affect downstream data analysis.
centroid	do the raw data files need to be centroided during conversion by MSConvert http://proteowizard.sourceforge.net/downloads.shtml. NB. centroiding of data is necessary for utilization of the "centWave" algorithm of xcms (findPeaks.centWave-methods).
MS2	logical should raw LC-MS data files converted by MSConvert to mzXml be converted as MS/MS files (e.g. data-dependent MS/MS files).

Details

MSConvert (ProteoWizard http://proteowizard.sourceforge.net/downloads.shtml) must be installed and in the case of windows in the path in the environmental variables. The mzXML file conversion will occur through shell commands using the command line version of MSConvert. If more than one cpu is utilized the mzXML file conversion process will occur as a parallel computation.

WMBEdmands/simExTargId documentation built on May 24, 2019, 2:08 a.m.