xcmsRaw {xcms} | R Documentation

## Constructor for xcmsRaw objects which reads NetCDF/mzXML files

### Description

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.

### Author(s)

Colin A. Smith, csmith@scripps.edu

### 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

### See Also

`xcmsRaw-class`, `profStep`, `profMethod` `xcmsFragments`

### Examples

    ## Not run:
        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)

    ## End(Not run)

[Package xcms version 3.16.1 Index]