EigenDecompose          EigenDecompose for the MNF analysis
LapackGenEigen          LapackGenEigen
MAF                     Class MAF
MCR-class               Class MCR
MNF                     Class MNF
MassImage               Class MassImage
MassSpectra             Class 'MassSpectra'
PCA-class               Class PCA
PCAnalysis              Class PCAnalysis
PeakList                Class PeakList
PrComp-class            Class PrComp
PrinComp-class          Class PrinComp
RSS                     generic accessor for RSS
RSS,MCR-method          MCR accessor RSS,
SNR                     Signal-to-Noise Ratio (SNR)
addFixedWidth           Generic method to add/update peak width
addPeaks                generic method to add peaks
analysis                'analysis', slot of 'MassSpectra' class objects
analysisName            'analysisName', slot of 'MassSpectra' class
                        objects
baseObject              generic accessor method baseObject
baseObject,PrComp-method
                        constructor for PrComp
baseObject,PrinComp-method
                        constructor for PrinComp
binning                 binning
bwApply                 bwApply
cReadRawPhi             Ulvac phi ToF-SIMS raw data import
calibPointNew           Generic method calibPointNew that modifies slot
                        calibPoints
calibPoints             'calibPoints', slot of 'MassSpectra' class
                        objects
calibration             'calibration', slot of 'MassSpectra' class
                        objects
changePeakWidth         method changePeakWidth
check.extension         Check file extension
computeMNF              compute MNF
computeNoise            computeNoise
coordToPixel            coordToPixel coordToPixel translates xy
                        coordinates from the locator() function to cell
                        coordinates from the image function. Origo is
                        according to ToF-SIMS images the upper left
                        corner.
coordToPixel,MassImage,numeric-method
                        coordToPixel
covDiffCalc             covDiffCalc calculates a x/y shift covariance
                        matrix of a multispectral image according to
                        Switzer and Green 1984.
ctable                  ctable is a C++ implementation to make
                        contingency tables
dim,MassImage-method    method dim for MassImage
dim,MassSpectra-method
                        method definition 'dim' for 'MassSpectra' dim
                        is a primitive
extract.header.data     extract variable names and values from
                        Ulvac-phi ToF-SIMS datafile headers
findClosestMatch        Find single value 'toMatch' in vector 'MatchIn'
findPeakWidth           generic method findPeakWidth
getTOFs                 generic method to calculate and get TOFs
image                   set a generic method for image
imageMatrix             generic method to obtain imageMatrix
import                  import is the C++ code for importing iontof raw
                        data
import.raw              Raw data import
instrument              'instrument', slot of 'MassSpectra' class
                        objects
iters                   generic accessor for iters slot
iters,MCR-method        MCR accessor iters,
itzipName               defining generic accessor method for
                        "itzipName"
itzipName<-             generic for setter itzipName
legend.col              legend.col
look.for.itzip.property
                        Get ITZIP property value
makeTIC                 generic for makeTIC
makeTIC,MassSpectra-method
                        Method makeTIC for MassSpectra Class
manualSelectPeaks       This method is base method for plotting and
                        manual select data
mz,MassSpectra-method   mz getter method
nComp                   generic accessor method for slot nComp
nPeaks                  generic method for nPeaks
ndim                    generic accessor method for slot ndim
ndim,MassSpectra-method
                        method definition 'ndim' on 'MassSpectra'
nearestNeighbourMean    nearestNeighbourMean
nnMNF                   Class nnMNF
nnMean                  nnMean is C++ code for calculating nearest
                        neighbour means in a 2D matrix
noPlottingData          generic method for 'noPlottingData' aka
                        'is.null'
noPlottingData,PCA-method
                        Check NULL PCA object
nz                      'nz', slot of 'MassSpectra' class objects
overlayPlot             generic overlayPlot
parIndicesSearch        helper function for parallel processing in
                        rawdata import routines
pcaLoadings             generic accessor for slot pcaLoadings
pcaMAF                  helper function for MAF calculation
pcaScores               generic accessor for slot pcaScores
peakIDs                 'peakIDs', slot of 'PeakList' class objects
peakMzs                 'peakMzs', slot of 'PeakList' class objects
peakPick                generic method peak.pick
peakWidths              Generic method peakWidths
peaks2Spectra           generic method peaks2Spectra
plot                    Generic method for plot
plot,MassImage,missing-method
                        Method 'plot()' for 'MassImage'
plot,PeakList,missing-method
                        Method 'plot()' for 'MassSpectra'
points                  generic method points generic method points
poissonScaling          generic method for "poissonScaling"
readBIF                 ToF-SIMS BIF/BIF6 file import
recalibrate             Generic method recalibrate
reduceSpectrumResolution
                        generic method reduceSpectrumResolution
removePeaks             generic method removePeaks
resids                  generic accessor method for resids
resids,MCR-method       MCR accessor resids,
scale                   generic for scale
show,MassImage-method   method definition 'show' on 'MassImage' show
                        has a generic by default
show,MassSpectra-method
                        method defining 'show()' for the 'MassSpectra'
                        class show has a generic by default
show,PeakList-method    method defining 'show()' for the 'MassSpectra'
                        class show has a generic by default
smoothScatter           generic for smoothScatter
smootherGolay           generic method smootherGolay
smootherSpline          generic smootherSpline
subset                  Generic method for subset
tofsims-package         ToF-SIMS Toolbox (tofsims)
unitMassPeaks           Generic method for unitMassPeaks
validMassImageObject    Validation method functionf for class MassImage
                        objects
validMassSpectraObject
                        Validation method function for class MassImage
                        objects
validPCAObject          Validation method function for class PCA
                        objects
validPeakListObject     Validation method function for class PeakList
                        objects
xdim                    generic accessor method for "xdim"
xdim,MassImage-method   Getter, method definition "xdim" on "MassImage"
xdim,PCA-method         method xdim() for PCA class object
xdim<-                  generic setter method for "xdim"
xy                      'xy', slot of 'MassImage' class objects
xySpec                  Generic method 'xySpec'
ydim                    generic accessor method for "ydim"
ydim,MassImage-method   Getter, method definition "ydim" on "MassImage"
ydim,PCA-method         method ydim() for PCA class object
ydim<-                  generic setter method for "ydim"
zdim                    generic accessor method for "zdim"
zdim,MassSpectra-method
                        method definition 'zdim' on 'MassSpectra'
