Changes in version 1.37.3 o Update within the tests only (not within the R code base): library database path for lvl spectral matching testing (required after removal of the local SQLite database from msPurityData). Changes in version 1.37.2 o Bug fix for subsetting the grouped data frame in the `average_xcms_grouped_msms_indiv` function Changes in version 1.37.1 o Removed library_spectra.db direct reference from msPurityData package (too large for Bioconductor) o spectralMatching() now downloads default library database from Zenodo (https://zenodo.org/records/18700802) and uses BiocFileCache with MD5 verification o spectral_matching() (deprecated function) now requires explicit library_db_pth parameter; default library no longer available o Added BiocFileCache to Imports for automatic caching of remote databases Changes in version 1.30.1 o Update example for purityX causing build error Changes in version 1.27.1 o createMSP fix - now uses the median precursor MZ and precursor RT in the MSP file Changes in version 1.21.2 o Fixes due to mz and intensity being named in columns for mzR and XCMS o Fixes for connection{base} file() opening changes (no longer accept w+a in function in R v4.2) o Update tests for the above o Update a reference of grpid in averageXFragSpectra functions more explicit (no change in functionality) o Typo fix in vignette Changes in version 1.21.1 o Bugfix for frag4feature for XCMS 3 compatability https://github.com/computational-metabolomics/msPurity/pull/93 o Remove imports that are no longer used Changes in version 1.19.2 o XCMS 3 compatability update (M-R-JONES) https://github.com/computational-metabolomics/msPurity/pull/91 Changes in version 1.19.1 o Bug fix for flagRemove (full width was not calculated as expected) Changes in version 1.17.2 o Update dev to match bug fixes in master Changes in version 1.17.1 o Update dev to match bug fixes in master Changes in version 1.16.2 o Author list updated Changes in version 1.16.1 o Update of createDatabase to record all intra average spectra in database o Add license and copyright info to code o Add github workflow CI (and subsequent formatting updates to pass tests) Changes in version 1.15.1 o Update dev to match bug fixes in master Changes in version 1.14.1 o Update of rdpc algorithm (see https://github.com/computational-metabolomics/msPurity/issues/78) o Update of align algorithm (see https://github.com/computational-metabolomics/msPurity/issues/79) o Fix for spectralMatching of type 'scan' previously incorrectly outputing no matches Changes in version 1.13.2 o Update dev to match bug fixes in master Changes in version 1.13.1 o Update dev to match bug fixes in master Changes in version 1.13.0 o Bioconductor dev (automatic version bump) Changes in version 1.12.2 o Fix to allow large files to be processed with combineAnnotation (in some cases the summary report should be excluded) Changes in version 1.12.1 o Bug fix for combineAnnotations - MS1 lookup not handling CAMERA adducts correctly o Fillpeaks bug fix see github #68 o Documentation fixes Changes in version 1.12.0 o Bioconductor release (automatic version bump) Changes in version 1.11.5 o frag4feature fileid fix for conversion from factor to character o Add missing plyr:: reference (thanks jsaintvanne) Changes in version 1.11.3 o Overhaul of combineAnnotation function. Uses local database now as previously API calls would take too much time to finish and was not usable o Various updates of createMSP to make compatible with Galaxy workflows o Parameter added to purityA to allow user to change the PPM tolerance for MZ values between scans when calculated the interpolated precursor ion purity o Update of spectralMatching results columns to include additional details (e.g. retention time) o 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 o Bug fix for EIC with MSMS data Changes in version 1.11.1 o Bug fix for duplicate MSP spectra when not using metadata table o Added xcms3 to xcmsSet conversion for "create database" code o Fix for sirius combine annotations (incorrect column format) Changes in version 1.11.0 o Bioconductor dev (automatic version bump) Changes in version 1.10.0 o Bioconductor release (automatic version bump) Changes in version 1.9.12 o Troublshoot mac "[MSData::Spectrum::getMZIntensityPairs()] Sizes do not match" error Changes in version 1.9.11 o Bug fix for createMSP - now handles metadata with duplicate grpids Changes in version 1.9.10 o Documentation updates Changes in version 1.9.9 o NEW FUNCTION: createDatabase o Updated version of create_database that uses an updated schema o NEW FUNCTION: spectralMatching o Updated version spectral_matching that allows for more flexibility o Vignettes and documentation update Changes in version 1.9.8 o NEW FUNCTION: filterFragSpectra (for purityA objects) o LC-MS/MS filtering of spectra (prior to averaging) o NEW FUNCTIONS: averageIntraFragSpectra, averageInterFragSpectra, averageAllFragSpectra (for purityA objects) o LC-MS/MS averaging and filtering functionality o NEW FUNCTION: createMSP o Create msp files from purityA objects where XCMS features have been linked to fragmentation spectra o Updated create_database and spectral matching to have the option to use averaged fragmentation spectra Changes in version 1.9.2 o 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) o Updated documentation for spectral matching Changes in version 1.7.6 o create_sql bug fix for msms spectra table. Was crashing due to incorrect ordering. o Add peak processing (flag remove peaks) for LC-MS XCMS data o 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 o 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 o Updates for database creation (can use CAMERA objects now) o 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 o Updates for Galaxy for Spectral Matching o Spectral matching ra_thres_t bugfix o 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 o Added very basic SIMS stitch compatibility o pcalc can handle NAs o Update of purityX to handle obiwarp RT correction (requires recording the RT RAW at an earlier step) o bug fix for when library spectra is bigger than target spectra (thanks Martin) Changes in version 1.3.1 o Add spectral matching functionality for LC-MS/MS Changes in version 1.1.1 o Added pcalc functions to be used by user o Added option to remove isotopes from calculation Changes in version 0.99.10 o Troubleshooting windows build failure Changes in version 0.99.9 o Offset bug fixed (previous only using extracting lower offset from mzML file) o Updated handling of RT corrected xcmsSet objects for frag4feature function o Additional column added for tracking ms/ms spectra Changes in version 0.99.8 o User option to change the mzR backend library Changes in version 0.99.4 o Troubleshooting mac build failure Changes in version 0.99.3 o Grouping multiple peaklist into one wide dataframe o Peaklists can now be averaged across each class using the function groupPeaks() for the class purityD o A list of dataframes can also be grouped together using the function groupPeakEx() Changes in version 0.99.2 o Updated class names purityPD to purityD o Updated class names purityLC to purityX o Updated vignette to reflect slightly different terminology o Added normalised TIC option for purityD msPurity v0.99.0 (Release date: 2016-04-08) o Initial release!