# Pre-Process, Visualize and Analyse Spectral Data

## Documentation for package ‘spectralAnalysis’ version 4.3.1

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

## Help Pages

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