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

addFixedWidthGeneric method to add/update peak width
addPeaksgeneric method to add peaks
analysis'analysis', slot of 'MassSpectra' class objects
analysisName'analysisName', slot of 'MassSpectra' class objects
baseObjectgeneric accessor method baseObject
baseObject-PrComp-methodconstructor for PrComp
baseObject-PrinComp-methodconstructor for PrinComp
calibPointNewGeneric method calibPointNew that modifies slot calibPoints
calibPoints'calibPoints', slot of 'MassSpectra' class objects
calibration'calibration', slot of 'MassSpectra' class objects
changePeakWidthmethod changePeakWidth
check.extensionCheck file extension
computeMNFcompute MNF
coordToPixelcoordToPixel coordToPixel translates xy coordinates from the...
covDiffCalccovDiffCalc calculates a x/y shift covariance matrix of a...
cReadRawPhiUlvac phi ToF-SIMS raw data import
ctablectable is a C++ implementation to make contingency tables
dim-MassImage-methodmethod dim for MassImage
dim-MassSpectra-methodmethod definition 'dim' for 'MassSpectra' dim is a primitive
EigenDecomposeEigenDecompose for the MNF analysis
extract.header.dataextract variable names and values from Ulvac-phi ToF-SIMS...
findClosestMatchFind single value 'toMatch' in vector 'MatchIn'
findPeakWidthgeneric method findPeakWidth
getTOFsgeneric method to calculate and get TOFs
imageset a generic method for image
imageMatrixgeneric method to obtain imageMatrix
importimport is the C++ code for importing iontof raw data
import.rawRaw data import
instrument'instrument', slot of 'MassSpectra' class objects
itersgeneric accessor for iters slot
iters-MCR-methodMCR accessor iters,
itzipNamedefining generic accessor method for "itzipName"
itzipName-setgeneric for setter itzipName
look.for.itzip.propertyGet ITZIP property value
makeTICgeneric for makeTIC
makeTIC-MassSpectra-methodMethod makeTIC for MassSpectra Class
manualSelectPeaksThis method is base method for plotting and manual select...
MassImageClass MassImage
MassSpectraClass 'MassSpectra'
mzmz getter method
nCompgeneric accessor method for slot nComp
ndimgeneric accessor method for slot ndim
ndim-MassSpectra-methodmethod definition 'ndim' on 'MassSpectra'
nnMeannnMean is C++ code for calculating nearest neighbour means in...
nnMNFClass nnMNF
noPlottingDatageneric method for 'noPlottingData' aka 'is.null'
noPlottingData-PCA-methodCheck NULL PCA object
nPeaksgeneric method for nPeaks
nz'nz', slot of 'MassSpectra' class objects
overlayPlotgeneric overlayPlot
parIndicesSearchhelper function for parallel processing in rawdata import...
PCA-classClass PCA
pcaLoadingsgeneric accessor for slot pcaLoadings
pcaMAFhelper function for MAF calculation
PCAnalysisClass PCAnalysis
pcaScoresgeneric accessor for slot pcaScores
peakIDs'peakIDs', slot of 'PeakList' class objects
PeakListClass PeakList
peakMzs'peakMzs', slot of 'PeakList' class objects
peakPickgeneric method peak.pick
peaks2Spectrageneric method peaks2Spectra
peakWidthsGeneric method peakWidths
plotGeneric method for plot
plot-MassImage-missing-methodMethod 'plot()' for 'MassImage'
plot-PeakList-missing-methodMethod 'plot()' for 'MassSpectra'
pointsgeneric method points generic method points
poissonScalinggeneric method for "poissonScaling"
PrCompClass PrComp
PrinCompClass PrinComp
readBIFToF-SIMS BIF/BIF6 file import
recalibrateGeneric method recalibrate
reduceSpectrumResolutiongeneric method reduceSpectrumResolution
removePeaksgeneric method removePeaks
residsgeneric accessor method for resids
resids-MCR-methodMCR accessor resids,
RSSgeneric accessor for RSS
RSS-MCR-methodMCR accessor RSS,
scalegeneric for scale
show-MassImage-methodmethod definition 'show' on 'MassImage' show has a generic by...
show-MassSpectra-methodmethod defining 'show()' for the 'MassSpectra' class show has...
show-PeakList-methodmethod defining 'show()' for the 'MassSpectra' class show has...
smootherGolaygeneric method smootherGolay
smootherSplinegeneric smootherSpline
smoothScattergeneric for smoothScatter
SNRSignal-to-Noise Ratio (SNR)
subsetGeneric method for subset
tofsims-packageToF-SIMS Toolbox (tofsims)
unitMassPeaksGeneric method for unitMassPeaks
validMassImageObjectValidation method functionf for class MassImage objects
validMassSpectraObjectValidation method function for class MassImage objects
validPCAObjectValidation method function for class PCA objects
validPeakListObjectValidation method function for class PeakList objects
xdimgeneric accessor method for "xdim"
xdim-MassImage-methodGetter, method definition "xdim" on "MassImage"
xdim-PCA-methodmethod xdim() for PCA class object
xdim-setgeneric setter method for "xdim"
xy'xy', slot of 'MassImage' class objects
xySpecGeneric method 'xySpec'
ydimgeneric accessor method for "ydim"
ydim-MassImage-methodGetter, method definition "ydim" on "MassImage"
ydim-PCA-methodmethod ydim() for PCA class object
ydim-setgeneric setter method for "ydim"
zdimgeneric accessor method for "zdim"
zdim-MassSpectra-methodmethod definition 'zdim' on 'MassSpectra'
tofsims documentation built on Nov. 8, 2020, 5:10 p.m.