xcms (version 1.48.0)

xcmsRaw: 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

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

Value

A xcmsRaw object.

Details

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.

References

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

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)