Constructor for xcmsRaw objects which reads NetCDF/mzXML files

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.

Usage

xcmsRaw(filename, profstep = 1, profmethod = "bin", profparam =
list(), includeMSn=FALSE, mslevel=NULL, scanrange=NULL)

deepCopy(object)

Arguments

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. See profile-matrix for details and supported values.
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)
mslevel: move data from mslevel into normal MS1 slots, e.g. for peak picking and visualisation
scanrange: scan range to read
object: An xcmsRaw object

Details

See profile-matrix for details on profile matrix generation methods and settings.

The scanrange to import can be restricted, otherwise all MS1 data is read. 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.

deepCopy(xraw) will create a copy of the xcmsRaw object with its own copy of mz and intensity data in xraw@env.

Value

A xcmsRaw object.

References

NetCDF file format: https://www.unidata.ucar.edu/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

Author

Colin A. Smith, csmith@scripps.edu

Examples

if (FALSE) {
    library(xcms)
    library(faahKO)
    cdfpath <- system.file("cdf", package = "faahKO")
    cdffiles <- list.files(cdfpath, recursive = TRUE, full.names = TRUE)
    xr<-xcmsRaw(cdffiles[1])
    xr
    ##This gives some information about the file
    names(attributes(xr))
    ## Lets have a look at the structure of the object

    str(xr)
    ##same but with a preview of each slot in the object
    ##SO... lets have a look at how this works
    head(xr@scanindex)
    ##[1]    0  429  860 1291 1718 2140
    xr@env$mz[425:430]
    ##[1] 596.3 597.0 597.3 598.1 599.3 200.1
    ##We can see that the 429 index is the last mz of scan 1 therefore...

    mz.scan1<-xr@env$mz[(1+xr@scanindex[1]):xr@scanindex[2]]
    intensity.scan1<-xr@env$intensity[(1+xr@scanindex[1]):xr@scanindex[2]]
    plot(mz.scan1, intensity.scan1, type="h",
         main=paste("Scan 1 of file", basename(cdffiles[1]), sep=""))
    ##the easier way :p
    scan1<-getScan(xr, 1)
    head(scan1)
    plotScan(xr, 1)
  }