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


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Documentation for package ‘tofsims’ version 1.15.0

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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)

-- A --

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

-- B --

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

-- C --

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

-- D --

dim-method method dim for MassImage
dim-method method definition 'dim' for 'MassSpectra' dim is a primitive

-- E --

EigenDecompose EigenDecompose for the MNF analysis
extract.header.data extract variable names and values from Ulvac-phi ToF-SIMS datafile headers

-- F --

findClosestMatch Find single value 'toMatch' in vector 'MatchIn'
findPeakWidth generic method findPeakWidth
findPeakWidth-method generic method findPeakWidth

-- G --

getTOFs generic method to calculate and get TOFs
getTOFs-method generic method to calculate and get TOFs

-- I --

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

-- L --

LapackGenEigen LapackGenEigen
legend.col legend.col
look.for.itzip.property Get ITZIP property value

-- M --

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

-- N --

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

-- O --

opaMCR Class MCR
overlayPlot generic overlayPlot
overlayPlot-method generic overlayPlot

-- P --

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

-- R --

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,

-- S --

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

-- U --

unitMassPeaks Generic method for unitMassPeaks
unitMassPeaks-method Generic method for unitMassPeaks

-- V --

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

-- X --

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'

-- Y --

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"

-- Z --

zdim generic accessor method for "zdim"
zdim-method method definition 'zdim' on 'MassSpectra'