A B C D E F G I L M N O P R S U V X Y Z
tofsims-package | ToF-SIMS Toolbox (tofsims) |
addFixedWidth | Generic method to add/update peak width |
addFixedWidth-method | Generic method to add/update peak width |
addPeaks | generic method to add peaks |
addPeaks-method | generic method to add peaks |
analysis | 'analysis', slot of 'MassSpectra' class objects |
analysis-method | 'analysis', slot of 'MassSpectra' class objects |
analysis<- | 'analysis', slot of 'MassSpectra' class objects |
analysis<--method | 'analysis', slot of 'MassSpectra' class objects |
analysisName | 'analysisName', slot of 'MassSpectra' class objects |
analysisName-method | 'analysisName', slot of 'MassSpectra' class objects |
analysisName<- | 'analysisName', slot of 'MassSpectra' class objects |
analysisName<--method | 'analysisName', slot of 'MassSpectra' class objects |
baseObject | generic accessor method baseObject |
baseObject-method | constructor for PrComp |
baseObject-method | constructor for PrinComp |
binning | binning |
binning-method | binning |
bwApply | bwApply |
bwApply-method | bwApply |
calibPointNew | Generic method calibPointNew that modifies slot calibPoints |
calibPointNew-method | Generic method calibPointNew that modifies slot calibPoints |
calibPoints | 'calibPoints', slot of 'MassSpectra' class objects |
calibPoints-method | 'calibPoints', slot of 'MassSpectra' class objects |
calibPoints<- | 'calibPoints', slot of 'MassSpectra' class objects |
calibPoints<--method | 'calibPoints', slot of 'MassSpectra' class objects |
calibration | 'calibration', slot of 'MassSpectra' class objects |
calibration-method | 'calibration', slot of 'MassSpectra' class objects |
calibration<- | 'calibration', slot of 'MassSpectra' class objects |
calibration<--method | 'calibration', slot of 'MassSpectra' class objects |
changePeakWidth | method changePeakWidth |
changePeakWidth-method | 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-method | coordToPixel |
covDiffCalc | covDiffCalc calculates a x/y shift covariance matrix of a multispectral image according to Switzer and Green 1984. |
cReadRawPhi | Ulvac phi ToF-SIMS raw data import |
cTable | ctable is a C++ implementation to make contingency tables |
ctable | ctable is a C++ implementation to make contingency tables |
dim-method | method dim for MassImage |
dim-method | method definition 'dim' for 'MassSpectra' dim is a primitive |
EigenDecompose | EigenDecompose for the MNF analysis |
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 |
findPeakWidth-method | generic method findPeakWidth |
getTOFs | generic method to calculate and get TOFs |
getTOFs-method | generic method to calculate and get TOFs |
image | set a generic method for image |
image-method | set a generic method for image |
imageMatrix | generic method to obtain imageMatrix |
imageMatrix-method | 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 |
instrument-method | 'instrument', slot of 'MassSpectra' class objects |
instrument<- | 'instrument', slot of 'MassSpectra' class objects |
instrument<--method | 'instrument', slot of 'MassSpectra' class objects |
iters | generic accessor for iters slot |
iters-method | MCR accessor iters, |
itzipName | defining generic accessor method for "itzipName" |
itzipName<- | generic for setter itzipName |
LapackGenEigen | LapackGenEigen |
legend.col | legend.col |
look.for.itzip.property | Get ITZIP property value |
MAF | Class MAF |
makeTIC | generic for makeTIC |
makeTIC-method | Method makeTIC for MassSpectra Class |
manualSelectPeaks | This method is base method for plotting and manual select data |
MassImage | Class MassImage |
MassSpectra | Class 'MassSpectra' |
MCR | Class MCR |
MCR-class | Class MCR |
MNF | Class MNF |
mz-method | mz getter method |
mz<--method | mz getter method |
nComp | generic accessor method for slot nComp |
nComp-method | generic accessor method for slot nComp |
ndim | generic accessor method for slot ndim |
ndim-method | method definition 'ndim' on 'MassSpectra' |
nearestNeighbourMean | nearestNeighbourMean |
nnMean | nnMean is C++ code for calculating nearest neighbour means in a 2D matrix |
nnMNF | Class nnMNF |
noPlottingData | generic method for 'noPlottingData' aka 'is.null' |
noPlottingData-method | Check NULL PCA object |
nPeaks | generic method for nPeaks |
nPeaks-method | generic method for nPeaks |
nz | 'nz', slot of 'MassSpectra' class objects |
nz-method | 'nz', slot of 'MassSpectra' class objects |
nz<- | 'nz', slot of 'MassSpectra' class objects |
nz<--method | 'nz', slot of 'MassSpectra' class objects |
opaMCR | Class MCR |
overlayPlot | generic overlayPlot |
overlayPlot-method | generic overlayPlot |
parIndicesSearch | helper function for parallel processing in rawdata import routines |
PCA | Class PCA |
PCA-class | Class PCA |
pcaLoadings | generic accessor for slot pcaLoadings |
pcaLoadings-method | generic accessor for slot pcaLoadings |
pcaMAF | helper function for MAF calculation |
PCAnalysis | Class PCAnalysis |
pcaScores | generic accessor for slot pcaScores |
pcaScores-method | generic accessor for slot pcaScores |
peakIDs | 'peakIDs', slot of 'PeakList' class objects |
peakIDs-method | 'peakIDs', slot of 'PeakList' class objects |
peakIDs<- | 'peakIDs', slot of 'PeakList' class objects |
peakIDs<--method | 'peakIDs', slot of 'PeakList' class objects |
PeakList | Class PeakList |
peakMzs | 'peakMzs', slot of 'PeakList' class objects |
peakMzs-method | 'peakMzs', slot of 'PeakList' class objects |
peakMzs<- | 'peakMzs', slot of 'PeakList' class objects |
peakMzs<--method | 'peakMzs', slot of 'PeakList' class objects |
peakPick | generic method peak.pick |
peakPick-method | generic method peak.pick |
peaks2Spectra | generic method peaks2Spectra |
peaks2Spectra-method | generic method peaks2Spectra |
peakWidths | Generic method peakWidths |
peakWidths-method | Generic method peakWidths |
plot | Generic method for plot |
plot-method | Method 'plot()' for 'MassImage' |
plot-method | Method 'plot()' for 'MassSpectra' |
plot-method | Generic method for plot |
points | generic method points generic method points |
points-method | generic method points generic method points |
poissonScaling | generic method for "poissonScaling" |
poissonScaling-method | generic method for "poissonScaling" |
PrComp | Class PrComp |
prComp | Class PrComp |
PrComp-class | Class PrComp |
PrinComp | Class PrinComp |
prinComp | Class PrinComp |
PrinComp-class | Class PrinComp |
readBIF | ToF-SIMS BIF/BIF6 file import |
recalibrate | Generic method recalibrate |
recalibrate-method | Generic method recalibrate |
reduceSpectrumResolution | generic method reduceSpectrumResolution |
reduceSpectrumResolution-method | generic method reduceSpectrumResolution |
removePeaks | generic method removePeaks |
removePeaks-method | generic method removePeaks |
resids | generic accessor method for resids |
resids-method | MCR accessor resids, |
RSS | generic accessor for RSS |
RSS-method | MCR accessor RSS, |
scale | generic for scale |
scale-method | generic for scale |
show-method | method definition 'show' on 'MassImage' show has a generic by default |
show-method | method defining 'show()' for the 'MassSpectra' class show has a generic by default |
show-method | method defining 'show()' for the 'MassSpectra' class show has a generic by default |
smootherGolay | generic method smootherGolay |
smootherGolay-method | generic method smootherGolay |
smootherSpline | generic smootherSpline |
smootherSpline-method | generic smootherSpline |
smoothScatter | generic for smoothScatter |
smoothScatter-method | generic for smoothScatter |
SNR | Signal-to-Noise Ratio (SNR) |
subset | Generic method for subset |
subset-method | Generic method for subset |
unitMassPeaks | Generic method for unitMassPeaks |
unitMassPeaks-method | 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-method | Getter, method definition "xdim" on "MassImage" |
xdim-method | method xdim() for PCA class object |
xdim<- | generic setter method for "xdim" |
xy | 'xy', slot of 'MassImage' class objects |
xy-method | 'xy', slot of 'MassImage' class objects |
xy<- | 'xy', slot of 'MassImage' class objects |
xy<--method | 'xy', slot of 'MassImage' class objects |
xySpec | Generic method 'xySpec' |
xySpec-method | Generic method 'xySpec' |
ydim | generic accessor method for "ydim" |
ydim-method | Getter, method definition "ydim" on "MassImage" |
ydim-method | method ydim() for PCA class object |
ydim<- | generic setter method for "ydim" |
zdim | generic accessor method for "zdim" |
zdim-method | method definition 'zdim' on 'MassSpectra' |