CHANGES IN VERSION 1.9.12 ========================= * Troublshoot mac "[MSData::Spectrum::getMZIntensityPairs()] Sizes do not match" error CHANGES IN VERSION 1.9.11 ========================= * Bug fix for createMSP - now handles metada with duplicate grpids CHANGES IN VERSION 1.9.10 ========================= * Documentation updates CHANGES IN VERSION 1.9.9 ========================= * NEW FUNCTION: createDatabase + Updated version of create_database that uses an updated schema * NEW FUNCTION: spectralMatching + Updated version spectral_matching that allows for more flexibility * Vigenettes and documentation update CHANGES IN VERSION 1.9.8 ========================= * NEW FUNCTION: filterFragSpectra (for purityA objects) + LC-MS/MS filtering of spectra (prior to averaging) * NEW FUNCTIONS: averageIntraFragSpectra, averageInterFragSpectra, averageAllFragSpectra (for purityA objects) + LC-MS/MS averaging and filtering functionality * NEW FUNCTION: createMSP + Create msp files from purityA objects where XCMS features have been linked to fragmentation spectra * Updated create_database and spectral matching to have the option to use averaged fragmentation spectra CHANGES IN VERSION 1.9.2 ========================= * Bug fix for groupPeaks and groupPeaksEx (the ppm argument was not working and there was inconsistent behaviour with larger datasets). Thanks to Elliot for spotting (https://github.com/litepalmer) * Updated documentation for spectral matching CHANGES IN VERSION 1.7.6 ========================= * create_sql bug fix for msms spectra table. Was crashing due to incorrect ordering. * Add peak processing (flag remove peaks) for LC-MS XCMS data * Add option to for frag4feature to just link to the grouped peak rtmin and rtmax (e.g. do not need to link to individual files) CHANGES IN VERSION 1.6.1 ========================= * Bug fix. For pos/neg switching acquisition two files are can be generated when converting from RAW to mzML (1 for pos, 1 for neg). The resulting files retention time scans were not being tracked properly in msPurity in these cases. This is now fixed. Thanks to Julien (https://github.com/jsaintvanne) for spotting the bug. CHANGES IN VERSION 1.5.1 ========================= * Updates for database creation (can use CAMERA objects now) * averageSpectra parameter 'MSFileReader' deprecated MSFileReader. Should use csvFile instead, MSFileReader option will still work but a warning will be given CHANGES IN VERSION 1.4.1/2/3 ========================= * Updates for Galaxy for Spectral Matching * Spectral matching ra_thres_t bugfix * Separation of sqlite database creation. Now can be called on it's own or with frag4feature (allows the Galaxy tool to be simplified) CHANGES IN VERSION 1.3.9 ========================= * Added very basic SIMS stitch compatibility * pcalc can handle NAs * Update of purityX to handle obiwarp RT correction (requires recording the RT RAW at an earlier step) * bug fix for when library spectra is bigger than target spectra (thanks Martin) CHANGES IN VERSION 1.3.1 ========================= * Add spectral matching functionality for LC-MS/MS CHANGES IN VERSION 1.1.1 ========================= * Added pcalc functions to be used by user * Added option to remove isotopes from calculation CHANGES IN VERSION 0.99.10/11/12 ========================= * Troubleshooting windows build failure CHANGES IN VERSION 0.99.9 ========================= * Offset bug fixed (previous only using extracting lower offset from mzML file) * Updated handling of RT corrected xcmsSet objects for frag4feature function * Additional column added for tracking ms/ms spectra CHANGES IN VERSION 0.99.8 ========================= * User option to change the mzR backend library CHANGES IN VERSION 0.99.4/5/6/7 ========================= * Troubleshooting mac build failure CHANGES IN VERSION 0.99.3 ========================= * Grouping multiple peaklist into one wide dataframe ** Peaklists can now be averaged across each class using the function groupPeaks() for the class purityD ** A list of dataframes can also be grouped togther using the function groupPeakEx() CHANGES IN VERSION 0.99.2 ========================= * Updated class names purityPD to purityD * Updated class names purityLC to purityX * Updated vignette to reflect slightly different terminology * Added normalised TIC option for purityD msPurity v0.99.0 (Release date: 2016-04-08) ========================= Initial release!