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