CHANGES IN VERSION 1.21.2 ========================= * Fixes due to mz and intensity being named in columns for mzR and XCMS * Fixes for connection{base} file() opening changes (no longer accept w+a in function in R v4.2) * Update tests for the above * Update a reference of grpid in averageXFragSpectra functions more explicit (no change in functionality) * Typo fix in vignette CHANGES IN VERSION 1.21.1 ========================= * Bugfix for frag4feature for XCMS 3 compatability https://github.com/computational-metabolomics/msPurity/pull/93 * Remove imports that are no longer used CHANGES IN VERSION 1.19.2 ========================= * XCMS 3 compatability update (M-R-JONES) https://github.com/computational-metabolomics/msPurity/pull/91 CHANGES IN VERSION 1.19.1 ========================= * Bug fix for flagRemove (full width was not calculated as expected) CHANGES IN VERSION 1.17.2 ========================= * Update dev to match bug fixes in master CHANGES IN VERSION 1.16.2 ========================= * Author list updated CHANGES IN VERSION 1.17.1 ========================= * Update dev to match bug fixes in master CHANGES IN VERSION 1.16.1 ========================= * Update of createDatabase to record all intra average spectra in database * Add license and copyright info to code * Add github workflow CI (and subsequent formatting updates to pass tests) CHANGES IN VERSION 1.15.1 ========================= * Update dev to match bug fixes in master CHANGES IN VERSION 1.14.1 ========================= * Update of rdpc algorithm (see https://github.com/computational-metabolomics/msPurity/issues/78) * Update of align algorithm (see https://github.com/computational-metabolomics/msPurity/issues/79) * Fix for spectralMatching of type 'scan' previously incorrectly outputing no matches CHANGES IN VERSION 1.13.2 ========================= * Update dev to match bug fixes in master CHANGES IN VERSION 1.12.2 ========================= * Fix to allow large files to be processed with combineAnnotation (in some cases the summary report should be excluded) CHANGES IN VERSION 1.13.1 ========================= * Update dev to match bug fixes in master CHANGES IN VERSION 1.12.1 ========================= * Bug fix for combineAnnotations - MS1 lookup not handling CAMERA adducts correctly * Fillpeaks bug fix see github #68 * Documentation fixes CHANGES IN VERSION 1.13.0 ========================= * Bioconductor dev (automatic version bump) CHANGES IN VERSION 1.12.0 ========================= * Bioconductor release (automatic version bump) CHANGES IN VERSION 1.11.5 ========================= * frag4feature fileid fix for conversion from factor to character * Add missing plyr:: reference (thanks jsaintvanne) CHANGES IN VERSION 1.11.3/4 ========================= * Overhaul of combineAnnotation function. Uses local database now as previously API calls would take too much time to finish and was not usable * Various updates of createMSP to make compatible with Galaxy workflows * Parameter added to purityA to allow user to change the PPM tolerance for MZ values between scans when calculated the interpolated precursor ion purity * Update of spectralMatching results columns to include additional details (e.g. retention time) * Update of spectralMatching so that either PostgreSQL or MySQL database can be used as input to either query or library CHANGES IN VERSION 1.11.2 ========================= * Bug fix for EIC with MSMS data CHANGES IN VERSION 1.11.1 ========================= * Bug fix for duplicate MSP spectra when not using metadata table * Added xcms3 to xcmsSet conversion for "create database" code * Fix for sirius combine annotations (incorrect column format) CHANGES IN VERSION 1.11.0 ========================= * Bioconductor dev (automatic version bump) CHANGES IN VERSION 1.10.0 ========================= * Bioconductor release (automatic version bump) 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 metadata 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 * Vignettes 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 together 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!