xcmsRaw {xcms} | R Documentation |
This function handles the task of reading a NetCDF/mzXML file containing
LC/MS or GC/MS data into a new xcmsRaw
object. It also
transforms the data into profile (maxrix) mode for efficient
plotting and data exploration.
xcmsRaw(filename, profstep = 1, profmethod = "intlin", profparam = list(), includeMSn=FALSE)
filename |
path name of the NetCDF or mzXML file to read |
profstep |
step size (in m/z) to use for profile generation |
profmethod |
method to use for profile generation |
profparam |
extra parameters to use for profile generation |
includeMSn |
only for XML file formats: also read MS$^n$ (Tandem-MS of Ion-/Orbi- Trap spectra) |
If profstep
is set to 0, no profile matrix is generated.
Unless includeMSn=TRUE only first level MS data is read, not MS/MS, etc.)
A xcmsRaw
object.
Colin A. Smith, csmith@scripps.edu
NetCDF file format: http://my.unidata.ucar.edu/content/software/netcdf/ http://www.astm.org/Standards/E2077.htm http://www.astm.org/Standards/E2078.htm
mzXML file format: http://sashimi.sourceforge.net/software_glossolalia.html
PSI-MS working group who developed mzData and mzML file formats: http://www.psidev.info/index.php?q=node/80
Parser used for XML file formats: http://tools.proteomecenter.org/wiki/index.php?title=Software:RAMP
xcmsRaw-class
,
profStep
,
profMethod
xcmsFragments