Description Usage Arguments Details Value Author(s) References See Also Examples
View source: R/functions-xcmsRaw.R
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.
1 2 3 4 |
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
|
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 |
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
.
A xcmsRaw
object.
Colin A. Smith, csmith@scripps.edu
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
xcmsRaw-class
,
profStep
,
profMethod
xcmsFragments
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 | ## 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)
|
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