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

This packages offers a pipeline for import, processing and analysis of ToF-SIMS 2D image data. Import of Iontof and Ulvac-Phi raw or preprocessed data is supported. For rawdata, mass calibration, peak picking and peak integration exist. General funcionality includes data binning, scaling, image subsetting and visualization. A range of multivariate tools common in the ToF-SIMS community are implemented (PCA, MCR, MAF, MNF). An interface to the bioconductor image processing package EBImage offers image segmentation functionality.

Author
Lorenz Gerber, Viet Mai Hoang
Date of publication
None
Maintainer
Lorenz Gerber <genfys@gmail.com>
License
GPL-3
Version
1.2.0

View on Bioconductor

Man pages

addFixedWidth
Generic method to add/update peak width
addPeaks
generic method to add peaks
analysis
'analysis', slot of 'MassSpectra' class objects
analysisName
'analysisName', slot of 'MassSpectra' class objects
baseObject
generic accessor method baseObject
baseObject-PrComp-method
constructor for PrComp
baseObject-PrinComp-method
constructor for PrinComp
binning
binning
bwApply
bwApply
calibPointNew
Generic method calibPointNew that modifies slot calibPoints
calibPoints
'calibPoints', slot of 'MassSpectra' class objects
calibration
'calibration', slot of 'MassSpectra' class objects
changePeakWidth
method changePeakWidth
check.extension
Check file extension
computeMNF
compute MNF
computeNoise
computeNoise
coordToPixel
coordToPixel coordToPixel translates xy coordinates from the...
coordToPixel-MassImage-numeric-method
coordToPixel
covDiffCalc
covDiffCalc calculates a x/y shift covariance matrix of a...
cReadRawPhi
Ulvac phi ToF-SIMS raw data import
ctable
ctable is a C++ implementation to make contingency tables
dim-MassImage-method
method dim for MassImage
dim-MassSpectra-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...
findClosestMatch
Find single value 'toMatch' in vector 'MatchIn'
findPeakWidth
generic method findPeakWidth
getTOFs
generic method to calculate and get TOFs
image
set a generic method for image
imageMatrix
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
iters
generic accessor for iters slot
iters-MCR-method
MCR accessor iters,
itzipName
defining generic accessor method for "itzipName"
itzipName-set
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-MassSpectra-method
Method makeTIC for MassSpectra Class
manualSelectPeaks
This method is base method for plotting and manual select...
MassImage
Class MassImage
MassSpectra
Class 'MassSpectra'
MCR
Class MCR
MNF
Class MNF
mz
mz getter method
nComp
generic accessor method for slot nComp
ndim
generic accessor method for slot ndim
ndim-MassSpectra-method
method definition 'ndim' on 'MassSpectra'
nearestNeighbourMean
nearestNeighbourMean
nnMean
nnMean is C++ code for calculating nearest neighbour means in...
nnMNF
Class nnMNF
noPlottingData
generic method for 'noPlottingData' aka 'is.null'
noPlottingData-PCA-method
Check NULL PCA object
nPeaks
generic method for nPeaks
nz
'nz', slot of 'MassSpectra' class objects
overlayPlot
generic overlayPlot
parIndicesSearch
helper function for parallel processing in rawdata import...
PCA-class
Class PCA
pcaLoadings
generic accessor for slot pcaLoadings
pcaMAF
helper function for MAF calculation
PCAnalysis
Class PCAnalysis
pcaScores
generic accessor for slot pcaScores
peakIDs
'peakIDs', slot of 'PeakList' class objects
PeakList
Class PeakList
peakMzs
'peakMzs', slot of 'PeakList' class objects
peakPick
generic method peak.pick
peaks2Spectra
generic method peaks2Spectra
peakWidths
Generic method peakWidths
plot
Generic method for plot
plot-MassImage-missing-method
Method 'plot()' for 'MassImage'
plot-PeakList-missing-method
Method 'plot()' for 'MassSpectra'
points
generic method points generic method points
poissonScaling
generic method for "poissonScaling"
PrComp
Class PrComp
PrinComp
Class PrinComp
readBIF
ToF-SIMS BIF/BIF6 file import
recalibrate
Generic method recalibrate
reduceSpectrumResolution
generic method reduceSpectrumResolution
removePeaks
generic method removePeaks
resids
generic accessor method for resids
resids-MCR-method
MCR accessor resids,
RSS
generic accessor for RSS
RSS-MCR-method
MCR accessor RSS,
scale
generic for scale
show-MassImage-method
method definition 'show' on 'MassImage' show has a generic by...
show-MassSpectra-method
method defining 'show()' for the 'MassSpectra' class show has...
show-PeakList-method
method defining 'show()' for the 'MassSpectra' class show has...
smootherGolay
generic method smootherGolay
smootherSpline
generic smootherSpline
smoothScatter
generic for smoothScatter
SNR
Signal-to-Noise Ratio (SNR)
subset
Generic method for subset
tofsims-package
ToF-SIMS Toolbox (tofsims)
unitMassPeaks
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-MassImage-method
Getter, method definition "xdim" on "MassImage"
xdim-PCA-method
method xdim() for PCA class object
xdim-set
generic setter method for "xdim"
xy
'xy', slot of 'MassImage' class objects
xySpec
Generic method 'xySpec'
ydim
generic accessor method for "ydim"
ydim-MassImage-method
Getter, method definition "ydim" on "MassImage"
ydim-PCA-method
method ydim() for PCA class object
ydim-set
generic setter method for "ydim"
zdim
generic accessor method for "zdim"
zdim-MassSpectra-method
method definition 'zdim' on 'MassSpectra'

Files in this package

tofsims/DESCRIPTION
tofsims/NAMESPACE
tofsims/NEWS
tofsims/R
tofsims/R/AllClassDefinition.R
tofsims/R/AllGenericDefinition.R
tofsims/R/AllGetters.R
tofsims/R/AllSetters.R
tofsims/R/MAF.R
tofsims/R/MCR.R
tofsims/R/MNF.R
tofsims/R/MassImage.R
tofsims/R/MassSpectra.R
tofsims/R/PCA.R
tofsims/R/PCAnalysis.R
tofsims/R/PeakList.R
tofsims/R/RcppExports.R
tofsims/R/importers.R
tofsims/R/prcomp.R
tofsims/R/princomp.R
tofsims/R/tofsims-package.R
tofsims/build
tofsims/build/vignette.rds
tofsims/inst
tofsims/inst/doc
tofsims/inst/doc/workflow.R
tofsims/inst/doc/workflow.Rmd
tofsims/inst/doc/workflow.html
tofsims/man
tofsims/man/EigenDecompose.Rd
tofsims/man/LapackGenEigen.Rd
tofsims/man/MAF.Rd
tofsims/man/MCR.Rd
tofsims/man/MNF.Rd
tofsims/man/MassImage.Rd
tofsims/man/MassSpectra.Rd
tofsims/man/PCA-class.Rd
tofsims/man/PCAnalysis.Rd
tofsims/man/PeakList.Rd
tofsims/man/PrComp.Rd
tofsims/man/PrinComp.Rd
tofsims/man/RSS-MCR-method.Rd
tofsims/man/RSS.Rd
tofsims/man/SNR.Rd
tofsims/man/addFixedWidth.Rd
tofsims/man/addPeaks.Rd
tofsims/man/analysis.Rd
tofsims/man/analysisName.Rd
tofsims/man/baseObject-PrComp-method.Rd
tofsims/man/baseObject-PrinComp-method.Rd
tofsims/man/baseObject.Rd
tofsims/man/binning.Rd
tofsims/man/bwApply.Rd
tofsims/man/cReadRawPhi.Rd
tofsims/man/calibPointNew.Rd
tofsims/man/calibPoints.Rd
tofsims/man/calibration.Rd
tofsims/man/changePeakWidth.Rd
tofsims/man/check.extension.Rd
tofsims/man/computeMNF.Rd
tofsims/man/computeNoise.Rd
tofsims/man/coordToPixel-MassImage-numeric-method.Rd
tofsims/man/coordToPixel.Rd
tofsims/man/covDiffCalc.Rd
tofsims/man/ctable.Rd
tofsims/man/dim-MassImage-method.Rd
tofsims/man/dim-MassSpectra-method.Rd
tofsims/man/extract.header.data.Rd
tofsims/man/findClosestMatch.Rd
tofsims/man/findPeakWidth.Rd
tofsims/man/getTOFs.Rd
tofsims/man/image.Rd
tofsims/man/imageMatrix.Rd
tofsims/man/import.Rd
tofsims/man/import.raw.Rd
tofsims/man/instrument.Rd
tofsims/man/iters-MCR-method.Rd
tofsims/man/iters.Rd
tofsims/man/itzipName-set.Rd
tofsims/man/itzipName.Rd
tofsims/man/legend.col.Rd
tofsims/man/look.for.itzip.property.Rd
tofsims/man/makeTIC-MassSpectra-method.Rd
tofsims/man/makeTIC.Rd
tofsims/man/manualSelectPeaks.Rd
tofsims/man/mz.Rd
tofsims/man/nComp.Rd
tofsims/man/nPeaks.Rd
tofsims/man/ndim-MassSpectra-method.Rd
tofsims/man/ndim.Rd
tofsims/man/nearestNeighbourMean.Rd
tofsims/man/nnMNF.Rd
tofsims/man/nnMean.Rd
tofsims/man/noPlottingData-PCA-method.Rd
tofsims/man/noPlottingData.Rd
tofsims/man/nz.Rd
tofsims/man/overlayPlot.Rd
tofsims/man/parIndicesSearch.Rd
tofsims/man/pcaLoadings.Rd
tofsims/man/pcaMAF.Rd
tofsims/man/pcaScores.Rd
tofsims/man/peakIDs.Rd
tofsims/man/peakMzs.Rd
tofsims/man/peakPick.Rd
tofsims/man/peakWidths.Rd
tofsims/man/peaks2Spectra.Rd
tofsims/man/plot-MassImage-missing-method.Rd
tofsims/man/plot-PeakList-missing-method.Rd
tofsims/man/plot.Rd
tofsims/man/points.Rd
tofsims/man/poissonScaling.Rd
tofsims/man/readBIF.Rd
tofsims/man/recalibrate.Rd
tofsims/man/reduceSpectrumResolution.Rd
tofsims/man/removePeaks.Rd
tofsims/man/resids-MCR-method.Rd
tofsims/man/resids.Rd
tofsims/man/scale.Rd
tofsims/man/show-MassImage-method.Rd
tofsims/man/show-MassSpectra-method.Rd
tofsims/man/show-PeakList-method.Rd
tofsims/man/smoothScatter.Rd
tofsims/man/smootherGolay.Rd
tofsims/man/smootherSpline.Rd
tofsims/man/subset.Rd
tofsims/man/tofsims-package.Rd
tofsims/man/unitMassPeaks.Rd
tofsims/man/validMassImageObject.Rd
tofsims/man/validMassSpectraObject.Rd
tofsims/man/validPCAObject.Rd
tofsims/man/validPeakListObject.Rd
tofsims/man/xdim-MassImage-method.Rd
tofsims/man/xdim-PCA-method.Rd
tofsims/man/xdim-set.Rd
tofsims/man/xdim.Rd
tofsims/man/xy.Rd
tofsims/man/xySpec.Rd
tofsims/man/ydim-MassImage-method.Rd
tofsims/man/ydim-PCA-method.Rd
tofsims/man/ydim-set.Rd
tofsims/man/ydim.Rd
tofsims/man/zdim-MassSpectra-method.Rd
tofsims/man/zdim.Rd
tofsims/src
tofsims/src/LapackEigen.cpp
tofsims/src/Makevars
tofsims/src/Makevars.win
tofsims/src/RcppExports.cpp
tofsims/src/c_importer.cpp
tofsims/src/nn.cpp
tofsims/src/readRawPhi.cpp
tofsims/src/tofsims_init.c
tofsims/src/utilities.cpp
tofsims/tests
tofsims/tests/testthat
tofsims/tests/testthat.R
tofsims/tests/testthat/test_MassImage.R
tofsims/tests/testthat/test_MassSpectra.R
tofsims/tests/testthat/test_PCA.R
tofsims/tests/testthat/test_import.R
tofsims/vignettes
tofsims/vignettes/rawimport.png
tofsims/vignettes/workflow.Rmd
tofsims/vignettes/workflow.bib