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

## Documentation for package ‘tofsims’ version 1.8.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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'