MassImage {tofsims} | R Documentation

## 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

### 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 <lorenz.gerber@slu.se>

### 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)

[Package tofsims version 1.16.0 Index]