![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
| assessPuritySingle | Assess the purity of a single LC-MS/MS or DI-MS/MS file |
| averageSpectra | Using purityD object, calculates to average mz, intensity and signal-to-noise of multiple scans from multiple MS datafiles (mzML or .csv) |
| averageSpectra-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) |
| create_database | Create database |
| dimsPredictPurity | Using purityD object, assess anticipated purity from a DI-MS run |
| dimsPredictPurity-method | Using purityD object, assess anticipated purity from a DI-MS run |
| dimsPredictPuritySingle | Predict the precursor purity from a DI-MS dataset |
| filterp | Filter out peaks based on intensity and RSD criteria |
| filterp-method | Filter out peaks based on intensity and RSD criteria |
| frag4feature | Assign precursor purity scored fragmentation spectra to XCMS features |
| frag4feature-method | Assign precursor purity scored fragmentation spectra to XCMS features |
| Getfiles | Get files for DI-MS processing |
| getP | Get peaklist for a purityD object |
| getP-method | Get peaklist for a purityD object |
| get_additional_mzml_meta | Get additional mzML meta |
| groupPeaks | Using purityD object, group multiple peaklists by similar mz values (mzML or .csv) |
| groupPeaks-method | Using purityD object, group multiple peaklists by similar mz values (mzML or .csv) |
| groupPeaksEx | Group peaklists from a list of dataframes |
| initialize-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 |
| pcalc | Perform purity calculation on a peak matrix |
| purityA | Assess the purity of multiple LC-MS/MS or DI-MS/MS files (constructor) |
| purityD | An S4 class to represent a DI-MS purityD |
| purityD-class | An S4 class to represent a DI-MS purityD |
| purityX | Assessing anticipated purity of XCMS features from an LC-MS run |
| show-method | Show method for purityA class |
| show-method | Show method for purityD |
| show-method | Show method for purityX |
| spectral_matching | Spectral matching |
| subtract | Using Subtract MZ values based on ppm tolerance and noise ratio |
| subtract-method | Using Subtract MZ values based on ppm tolerance and noise ratio |
| subtractMZ | Subtract MZ values based on ppm tolerance and noise ratio |
| validate | Validate precursor purity predictions using LC-MS and LC-MS/MS dataset |
| validate-method | Validate precursor purity predictions using LC-MS and LC-MS/MS dataset |
| writeOut | Using purityD object, save peaks as text files |
| writeOut-method | Using purityD object, save peaks as text files |