Getfiles                Get files for DI-MS processing
assessPuritySingle      Assess the purity of a single LC-MS/MS or
                        DI-MS/MS file
averageAllFragSpectra,purityA-method
                        Using a purityA object, average and filter
                        MS/MS spectra for each XCMS feature within and
                        across MS data files (ignoring intra and inter
                        relationships)
averageInterFragSpectra,purityA-method
                        Using a purityA object, average and filter
                        fragmentation spectra for each XCMS feature
                        across multiple MS data files
averageIntraFragSpectra,purityA-method
                        Using a purityA object, average and filter
                        fragmentation spectra for each XCMS feature
                        within a MS data file
averageSpectra,purityD-method
                        Using purityD object, calculates to average mz,
                        intensity and signal-to-noise of multiple scans
                        from multiple MS datafiles (mzML or .csv)
averageSpectraSingle    Calculates to average mz, intensity and
                        signal-to-noise of multiple scans from 1 MS
                        datafile (mzML or .csv)
combineAnnotations      Combine Annotations
createDatabase          Create database
createMSP,purityA-method
                        Using a purityA object, create an MSP file of
                        fragmentation spectra
create_database         Create database deprecated
dimsPredictPurity,purityD-method
                        Using purityD object, assess anticipated purity
                        from a DI-MS run
dimsPredictPuritySingle
                        Predict the precursor purity from a DI-MS
                        dataset
filterFragSpectra,purityA-method
                        Filter fragmentation spectra associated with an
                        XCMS feature
filterp,purityD-method
                        Filter out peaks based on intensity and RSD
                        criteria
flag_remove             Flag and remove unwanted peaks
frag4feature,purityA-method
                        Using a purityA object, link MS/MS data to XCMS
                        features
getP,purityD-method     Get peaklist for a purityD object
get_additional_mzml_meta
                        Get additional mzML meta
groupPeaks,purityD-method
                        Using purityD object, group multiple peaklists
                        by similar mz values (mzML or .csv)
groupPeaksEx            Group peaklists from a list of dataframes
initialize,purityD-method
                        Constructor for S4 class to represent a DI-MS
                        purityD
iwNormGauss             Gaussian normalisation for isolation window
                        efficiency
iwNormQE.5              Q-Exactive +/- 0.5 range, normalisation for
                        isolation window efficiency
iwNormRcosine           Raised cosine normalisation for isolation
                        window efficiency
msPurity                'msPurity' package
pcalc                   Perform purity calculation on a peak matrix
purityA                 Assess the acquired precursor ion purity of
                        MS/MS spectra (constructor)
purityD-class           An S4 class to represent a DI-MS purityD
purityX                 Assessing anticipated purity of XCMS features
                        from an LC-MS run
show,purityA-method     Show method for purityA class
show,purityD-method     Show method for purityD
show,purityX-method     Show method for purityX
spectralMatching        Spectral matching for LC-MS/MS datasets
spectral_matching       Spectral matching deprecated
subtract,purityD-method
                        Using Subtract MZ values based on ppm tolerance
                        and noise ratio
subtractMZ              Subtract MZ values based on ppm tolerance and
                        noise ratio
validate,purityA-method
                        Validate precursor purity predictions using
                        LC-MS and LC-MS/MS dataset
writeOut,purityD-method
                        Using purityD object, save peaks as text files
