MassImage: Class MassImage

In tofsims: Import, process and analysis of Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) imaging data

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

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.

Value

object of class MassImage

Slots

xy

vector giving the pixel dimension of the image

Author(s)

Lorenz Gerber <[e-mail]>

Examples

# 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)

tofsims documentation built on Nov. 8, 2020, 5:10 p.m.