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.

AuthorLorenz Gerber, Viet Mai Hoang
Date of publicationNone
MaintainerLorenz Gerber <genfys@gmail.com>
LicenseGPL-3
Version1.2.0

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

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