Pre-Process, Visualize and Analyse Spectral Data

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Documentation for package ‘spectralAnalysis’ version 4.3.3

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baselineCorrect generic function to perfom baseline correction
baselineCorrect-method generic function to perfom baseline correction
checkCompatible Check object compatibility
checkCompatible-method Check object compatibility
checkForRedundantSources Check for redunt NMF source vectors
checkIdenticalClass check wether all elements of of the same class
combineSpectralObjects Function to combine 'SpectraInTime-class' objects containing 1 spectrum each
computeNMFResidu NMF relative residual per observation
e Create an 'ElementsToSelect-class' from a numeric vector or multiple numeric values or vectors
ElementsToSelect-class Elements S4 class useful for closest elements subsetting
firstSpectrum Get the first spectrum
firstSpectrum-method Get the first spectrum
getDefaultSumFunc function to get default summary functions
getDefaultTimeFormat function to get default time format in the package
getDimensionReduction generic function to extract 'dimensionReduction'-slot
getDimensionReduction-method SpectraInTimeComp-class (time resolved spectra )
getElements generic function to extract 'elements'-slot
getElements-method generic function to extract 'elements'-slot
getExperimentName generic function to extract 'experimentName'-slot
getExperimentName-method generic function to extract 'experimentName'-slot
getExtraInfo generic function to extract 'extraInfo'-slot
getExtraInfo-method generic function to extract 'extraInfo'-slot
getListOfSpectraExample get example list of spectra
getNMFInputMatrix Get spectralData as input NMF model
getPathProcessTimesExample example path process times
getPreprocessing generic function to extract 'preprocessing'-slot
getPreprocessing-method generic function to extract 'preprocessing'-slot
getProcessTimesExample get a minimal 'ProcessTimes-class' example based on 'getSpectraInTimeExample'
getProcessTimesFrameExample get mimimal example 'ProcessTimesFrame-class'
getRange generic function to extract 'range'-slot
getRange-method generic function to extract 'range'-slot
getSpectra generic function to extract 'spectra'-slot
getSpectra-method generic function to extract 'spectra'-slot
getSpectraInTimeCompExample Artificial example of 'SpectraInTimeComp-class'
getSpectraInTimeExample Artificial example 'SpectraInTime-class'
getSpectralAxis generic function to extract 'spectralAxis'-slot
getSpectralAxis-method generic function to extract 'spectralAxis'-slot
getStartTime generic function to extract 'startTime'-slot
getStartTime-method generic function to extract 'startTime'-slot
getTimePoints generic function to extract 'timePoints'-slot
getTimePoints-method generic function to extract 'timePoints'-slot
getUnits generic function to extract 'units'-slot
getUnits-method generic function to extract 'units'-slot
includeRedundantSources Re-introduce redundant sources in NMF-model
initializeNMFModel Initialize NMF model with initial spectral data
lastSpectrum Get the last spectrum
lastSpectrum-method Get the last spectrum
loadAllSPCFiles Load all or a selection of SPC files from a given directory.
localBaselineCorrect Local baseline correction
nonNegativePreprocessing condition datamatrix to input in and condition properly for NMF
normalize generic normalization function
normalize-method generic normalization function
predictNNLS Based on previously obtained NMF result 'NMFResult', estimate coefficients for a new spectralData object 'object' using non-negative least squares fitting. The result is returned as as an NMF model.
preprocess generic function to preprocess an S4 object
preprocess-method generic function to preprocess an S4 object
ProcessTimes S4 Class key process times
ProcessTimes-class S4 Class key process times
ProcessTimesFrame-class ProcessTimes-class
r create a 'RangeToSubset-class' object from 2 elements or from a vector
r-method create a 'RangeToSubset-class' object from 2 elements or from a vector
RangeToSubset RangeToSubset-class
Rangetosubset RangeToSubset-class
rangetosubset RangeToSubset-class
RangeToSubset-class RangeToSubset-class
read read or save a 'SpectraInTime-class' from or to a '.txt' file
readProcessTimes read .csv file as process times
readSPC Read-in of a SPC file.
readSpectra read or save a 'SpectraInTime-class' from or to a '.txt' file
removeRedundantSources Remove redundant sources from the initial NMF model
runNMF Actual NMF analysis
save read or save a 'SpectraInTime-class' from or to a '.txt' file
saveSpectra read or save a 'SpectraInTime-class' from or to a '.txt' file
scaleNMFResult Apply fixed scaling to NMF model
setExperimentName<- set the experiment name
setExperimentName<--method set the experiment name
setTimePointsAlt<- set time alternative time axis
setTimePointsAlt<--method set the experiment name
smooth generic smoothing function
smooth-method generic smoothing function
SpectraInTimeComp SpectraInTimeComp-class (time resolved spectra )
spectraInTimeComp SpectraInTimeComp-class (time resolved spectra )
spectraintimecomp SpectraInTimeComp-class (time resolved spectra )
SpectraInTimeComp-class SpectraInTimeComp-class (time resolved spectra )
spectralIntegration Integrate spectraInTime object
spectralNMF Perform Non-Negative Matrix factorization on spectral data
spectralNMFList Perform Non-Negative Matrix factorization on list of SPC files
spectralPLSCalibration Compute PLS model
spectralPlsPrediction Perform PLS prediction
subset-methods Subsetting 'SpectraInTime-class'
TemperatureInfo S4 Class key process times
temperatureInfo S4 Class key process times
temperatureinfo S4 Class key process times
timeAlign Time align first object, using info in the second object
timeAlign-method Time align first object, using info in the second object
upsampleNMFResult Upsample NMF result to original temporal resolution
wavelengthAlign Wavelength align spectral data
wavelengthAlign-method Wavelength align spectral data
[-method Subsetting 'SpectraInTime-class'
[ProcessTimes-method Check object compatibility
[SpectraInTime-method Check object compatibility