tofsims (version 1.0.2)

MassImage: Class MassImage

Description

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.

Usage

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, ...)

Arguments

select

character, 'ulvacbif', 'iontofbif', 'iontofgrdpeaks', 'ulvacrawpeaks', 'dummy'

analysisName

character, name of analysis

PeakListobj

PeakList class object, used as peaklist for rawdata import

untilScan

integer or NULL to determine number of ToF-SIMS scans to import

...

additional args

Value

• object of class MassImage

Details

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.

Examples

# creating dummy data
testImage<-MassImage('dummy')
image(testImage)
# 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)