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tofsims (version 1.0.2)

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

Description

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.

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Version

Version

1.0.2

License

GPL-3

Maintainer

Lorenz Gerber

Last Published

February 15th, 2017

Functions in tofsims (1.0.2)

import is the C++ code for importing iontof raw data

EigenDecompose for the MNF analysis

Class MassImage

generic accessor method for slot nComp

Class MassSpectra

Generic method to add/update peak width

Generic method calibPointNew that modifies slot calibPoints

generic method points generic method points

findClosestMatch

Find single value 'toMatch' in vector 'MatchIn'

generic accessor method for slot ndim

dim,MassSpectra-method

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

Class PCAnalysis

analysisName, slot of MassSpectra class objects

generic overlayPlot

generic method for nPeaks

zdim,MassSpectra-method

method definition 'zdim' on 'MassSpectra'

calibPoints, slot of MassSpectra class objects

generic accessor for RSS

parIndicesSearch

helper function for parallel processing in rawdata import routines

changePeakWidth

method changePeakWidth

noPlottingData,PCA-method

Check NULL PCA object

MCR accessor RSS,

Raw data import

check.extension

Check file extension

baseObject,PrComp-method

constructor for PrComp

defining generic accessor method for "itzipName"

ndim,MassSpectra-method

method definition 'ndim' on 'MassSpectra'

nearestNeighbourMean

nearestNeighbourMean

extract.header.data

extract variable names and values from Ulvac-phi ToF-SIMS datafile headers

baseObject,PrinComp-method

constructor for PrinComp

generic method findPeakWidth

generic method removePeaks

generic accessor for iters slot

coordToPixel,MassImage,numeric-method

generic for setter itzipName

generic method to obtain imageMatrix

ydim,MassImage-method

Getter, method definition "ydim" on "MassImage"

Generic method recalibrate

ctable is a C++ implementation to make contingency tables

manualSelectPeaks

This method is base method for plotting and manual select data

generic method for 'noPlottingData' aka 'is.null'

show,PeakList-method

method defining show() for the MassSpectra class show has a generic by default

show,MassImage-method

method definition 'show' on 'MassImage' show has a generic by default

generic method for "poissonScaling"

show,MassSpectra-method

method defining show() for the MassSpectra class show has a generic by default

generic accessor method for "ydim"

Generic method for plot

nnMean is C++ code for calculating nearest neighbour means in a 2D matrix

xy, slot of MassImage class objects

peakMzs, slot of PeakList class objects

generic accessor method baseObject

validMassImageObject

Validation method functionf for class MassImage objects

xdim,MassImage-method

Getter, method definition "xdim" on "MassImage"

generic accessor method for "xdim"

set a generic method for image

Generic method xySpec

generic setter method for "ydim"

Generic method for unitMassPeaks

instrument, slot of MassSpectra class objects

nz, slot of MassSpectra class objects

generic accessor method for resids

generic method peak.pick

xdim,PCA-method

method xdim() for PCA class object

mz,MassSpectra-method

mz getter method

Generic method peakWidths

generic method smootherGolay

peakIDs, slot of PeakList class objects

generic method to calculate and get TOFs

generic accessor for slot pcaScores

generic setter method for "xdim"

generic accessor method for "zdim"

makeTIC,MassSpectra-method

Method makeTIC for MassSpectra Class

generic smootherSpline

analysis, slot of MassSpectra class objects

calibration, slot of MassSpectra class objects

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.

validMassSpectraObject

Validation method function for class MassImage objects

Validation method function for class PCA objects

resids,MCR-method

MCR accessor resids,

tofsims-package

ToF-SIMS Toolbox (tofsims)

ydim,PCA-method

method ydim() for PCA class object

Signal-to-Noise Ratio (SNR)

covDiffCalc calculates a x/y shift covariance matrix of a multispectral image according to Switzer and Green 1984.

dim,MassImage-method

method dim for MassImage

generic for makeTIC

generic accessor for slot pcaLoadings

generic method to add peaks

plot,MassImage,missing-method

Method plot() for MassImage

generic method peaks2Spectra

plot,PeakList,missing-method

Method plot() for MassSpectra

generic for smoothScatter

validPeakListObject

Validation method function for class PeakList objects

iters,MCR-method

MCR accessor iters,

Ulvac phi ToF-SIMS raw data import

helper function for MAF calculation

look.for.itzip.property

Get ITZIP property value

ToF-SIMS BIF/BIF6 file import

generic for scale

Generic method for subset

reduceSpectrumResolution

generic method reduceSpectrumResolution