MassImage {tofsims} | R Documentation |
Class MassImage contains the information to shape a number of mass spectra into an image.
MassImage
is also the call to the class constructor. It is used for
importing both BIF/BIF6 and raw image data.
MassImage(select = c("ulvacbif", "iontofbif", "iontofgrdpeaks", "ulvacrawpeaks", "dummy"), analysisName, PeakListobj = c(), untilScan = NULL, ...) MassImage(select = c("ulvacbif", "iontofbif", "iontofgrdpeaks", "ulvacrawpeaks", "dummy"), analysisName, PeakListobj = c(), untilScan = NULL, ...)
select |
|
analysisName |
|
PeakListobj |
|
untilScan |
integer or NULL to determine number of ToF-SIMS scans to import |
... |
additional args |
Class MassImage
inherits from the classes MassAnalysis
and
MassSpectra
. It contains the information to shape a number of mass
spectra into an image.
MassImage
is the user class constructor to obtain a MassImage object.
Data can be imported from BIF or raw data files (Iontof or Ulvacphi). To
import raw data, a MassSpectra object with a valid PeakList object has to
be provided as argument.
object of class MassImage
xy
vector giving the pixel dimension of the image
Lorenz Gerber <lorenz.gerber@slu.se>
# creating dummy data testImage<-MassImage('dummy') image(testImage) ## Not run: # import of rawdata # first a PeakList object has to be created library(tofsimsData) data(tofsimsData) testSpectra <- calibPointNew(testSpectra, mz = 15, value = 15.01551) testSpectra <- calibPointNew(testSpectra, mz = 181, value = 181.0228) testSpectra <- recalibrate(testSpectra) testSpectra <- unitMassPeaks(testSpectra, mzRange = c(1,200), widthAt = c(15, 181), factor = c(0.4, 0.6), lower = c(14.97, 15.05), upper = c(180.84, 181.43)) # obtaining the path to the raw data file in 'tofsims' package importFile<-system.file("rawdata", "trift_test_001.RAW", package = "tofsimsData") rawImportedImage <- MassImage('ulvacrawpeaks', importFile, PeakListobj = testSpectra) image(rawImportedImage) ## End(Not run)