| 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... |
| averageInterFragSpectra-purityA-method | Using a purityA object, average and filter fragmentation... |
| averageIntraFragSpectra-purityA-method | Using a purityA object, average and filter fragmentation... |
| averageSpectra-purityD-method | Using purityD object, calculates to average mz, intensity and... |
| averageSpectraSingle | Calculates to average mz, intensity and signal-to-noise of... |
| combineAnnotations | Combine Annotations |
| create_database | Create database deprecated |
| createDatabase | Create database |
| createMSP-purityA-method | Using a purityA object, create an MSP file of fragmentation... |
| dimsPredictPurity-purityD-method | Using purityD object, assess anticipated purity from a DI-MS... |
| dimsPredictPuritySingle | Predict the precursor purity from a DI-MS dataset |
| filterFragSpectra-purityA-method | Filter fragmentations 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 |
| get_additional_mzml_meta | Get additional mzML meta |
| Getfiles | Get files for DI-MS processing |
| getP-purityD-method | Get peaklist for a purityD object |
| groupPeaksEx | Group peaklists from a list of dataframes |
| groupPeaks-purityD-method | Using purityD object, group multiple peaklists by similar mz... |
| 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... |
| 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... |
| purityD-class | An S4 class to represent a DI-MS purityD |
| purityX | Assessing anticipated purity of XCMS features from an LC-MS... |
| show-purityA-method | Show method for purityA class |
| show-purityD-method | Show method for purityD |
| show-purityX-method | Show method for purityX |
| spectral_matching | Spectral matching deprecated |
| spectralMatching | Spectral matching for LC-MS/MS datasets |
| subtractMZ | Subtract MZ values based on ppm tolerance and noise ratio |
| subtract-purityD-method | Using Subtract MZ values based on ppm tolerance and noise... |
| validate-purityA-method | Validate precursor purity predictions using LC-MS and... |
| writeOut-purityD-method | Using purityD object, save peaks as text files |
