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@@ -2,8 +2,8 @@ Package: msPurity | |
| Type: Package | ||
| Title: Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based | ||
| Fragmentation in Metabolomics | ||
| Version: 1.21.2 | ||
| Date: 2022-04-12 | ||
| Version: 1.27.1 | ||
| Date: 2023-08-30 | ||
| Authors@R: c( | ||
| person(given = "Thomas N.", family = "Lawson", | ||
| email = "[email protected]", role = c("aut", "cre"), | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,219 +1,181 @@ | ||
| CHANGES IN VERSION 1.27.1 | ||
| + createMSP fix - now uses outputs the median precursor MZ and precursor intensity in the MSP file | ||
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| 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 | ||
| + 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 | ||
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| 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 | ||
| + Bugfix for frag4feature for XCMS 3 compatability https://github.com/computational-metabolomics/msPurity/pull/93 | ||
| + Remove imports that are no longer used | ||
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| CHANGES IN VERSION 1.19.2 | ||
| ========================= | ||
| * XCMS 3 compatability update (M-R-JONES) https://github.com/computational-metabolomics/msPurity/pull/91 | ||
| + XCMS 3 compatability update (M-R-JONES) https://github.com/computational-metabolomics/msPurity/pull/91 | ||
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| CHANGES IN VERSION 1.19.1 | ||
| ========================= | ||
| * Bug fix for flagRemove (full width was not calculated as expected) | ||
| + Bug fix for flagRemove (full width was not calculated as expected) | ||
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| CHANGES IN VERSION 1.17.2 | ||
| ========================= | ||
| * Update dev to match bug fixes in master | ||
| + Update dev to match bug fixes in master | ||
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| CHANGES IN VERSION 1.16.2 | ||
| ========================= | ||
| * Author list updated | ||
| + Author list updated | ||
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| CHANGES IN VERSION 1.17.1 | ||
| ========================= | ||
| * Update dev to match bug fixes in master | ||
| + Update dev to match bug fixes in master | ||
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| 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) | ||
| + 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) | ||
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| CHANGES IN VERSION 1.15.1 | ||
| ========================= | ||
| * Update dev to match bug fixes in master | ||
| + Update dev to match bug fixes in master | ||
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| 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 | ||
| + 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 | ||
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| CHANGES IN VERSION 1.13.2 | ||
| ========================= | ||
| * Update dev to match bug fixes in master | ||
| + Update dev to match bug fixes in master | ||
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| 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) | ||
| + Fix to allow large files to be processed with combineAnnotation (in some cases the summary report should be excluded) | ||
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| CHANGES IN VERSION 1.13.1 | ||
| ========================= | ||
| * Update dev to match bug fixes in master | ||
| + Update dev to match bug fixes in master | ||
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| 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 | ||
| + Bug fix for combineAnnotations - MS1 lookup not handling CAMERA adducts correctly | ||
| + Fillpeaks bug fix see github #68 | ||
| + Documentation fixes | ||
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| CHANGES IN VERSION 1.13.0 | ||
| ========================= | ||
| * Bioconductor dev (automatic version bump) | ||
| + Bioconductor dev (automatic version bump) | ||
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| CHANGES IN VERSION 1.12.0 | ||
| ========================= | ||
| * Bioconductor release (automatic version bump) | ||
| + Bioconductor release (automatic version bump) | ||
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| CHANGES IN VERSION 1.11.5 | ||
| ========================= | ||
| * frag4feature fileid fix for conversion from factor to character | ||
| * Add missing plyr:: reference (thanks jsaintvanne) | ||
| + frag4feature fileid fix for conversion from factor to character | ||
| + Add missing plyr:: reference (thanks jsaintvanne) | ||
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| CHANGES IN VERSION 1.11.3/4 | ||
| ========================= | ||
| * Overhaul of combineAnnotation function. Uses local database now as previously | ||
| + 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 | ||
| + 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 | ||
| + 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 | ||
| + Update of spectralMatching so that either PostgreSQL or MySQL database can be | ||
| used as input to either query or library | ||
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| CHANGES IN VERSION 1.11.2 | ||
| ========================= | ||
| * Bug fix for EIC with MSMS data | ||
| + Bug fix for EIC with MSMS data | ||
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| 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) | ||
| + 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) | ||
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| CHANGES IN VERSION 1.11.0 | ||
| ========================= | ||
| * Bioconductor dev (automatic version bump) | ||
| + Bioconductor dev (automatic version bump) | ||
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| CHANGES IN VERSION 1.10.0 | ||
| ========================= | ||
| * Bioconductor release (automatic version bump) | ||
| + Bioconductor release (automatic version bump) | ||
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| CHANGES IN VERSION 1.9.12 | ||
| ========================= | ||
| * Troublshoot mac "[MSData::Spectrum::getMZIntensityPairs()] Sizes do not match" error | ||
| + Troublshoot mac "[MSData::Spectrum::getMZIntensityPairs()] Sizes do not match" error | ||
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| CHANGES IN VERSION 1.9.11 | ||
| ========================= | ||
| * Bug fix for createMSP - now handles metadata with duplicate grpids | ||
| + Bug fix for createMSP - now handles metadata with duplicate grpids | ||
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| CHANGES IN VERSION 1.9.10 | ||
| ========================= | ||
| * Documentation updates | ||
| + Documentation updates | ||
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| 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 | ||
| + NEW FUNCTION: createDatabase | ||
| o Updated version of create_database that uses an updated schema | ||
| + NEW FUNCTION: spectralMatching | ||
| o Updated version spectral_matching that allows for more flexibility | ||
| + Vignettes and documentation update | ||
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| 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 | ||
| + NEW FUNCTION: filterFragSpectra (for purityA objects) | ||
| o LC-MS/MS filtering of spectra (prior to averaging) | ||
| + NEW FUNCTIONS: averageIntraFragSpectra, averageInterFragSpectra, averageAllFragSpectra (for purityA objects) | ||
| o LC-MS/MS averaging and filtering functionality | ||
| + NEW FUNCTION: createMSP | ||
| o 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 | ||
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| 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 | ||
| + 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 | ||
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| 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) | ||
| + 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) | ||
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| 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 | ||
| + 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. | ||
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| 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 | ||
| + 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 | ||
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| 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 | ||
| + 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) | ||
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| 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) | ||
| + 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) | ||
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| CHANGES IN VERSION 1.3.1 | ||
| ========================= | ||
| * Add spectral matching functionality for LC-MS/MS | ||
| + Add spectral matching functionality for LC-MS/MS | ||
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| CHANGES IN VERSION 1.1.1 | ||
| ========================= | ||
| * Added pcalc functions to be used by user | ||
| * Added option to remove isotopes from calculation | ||
| + Added pcalc functions to be used by user | ||
| + Added option to remove isotopes from calculation | ||
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| CHANGES IN VERSION 0.99.10/11/12 | ||
| ========================= | ||
| * Troubleshooting windows build failure | ||
| + Troubleshooting windows build failure | ||
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| 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 | ||
| + 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 | ||
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| CHANGES IN VERSION 0.99.8 | ||
| ========================= | ||
| * User option to change the mzR backend library | ||
| + User option to change the mzR backend library | ||
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| CHANGES IN VERSION 0.99.4/5/6/7 | ||
| ========================= | ||
| * Troubleshooting mac build failure | ||
| + Troubleshooting mac build failure | ||
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| 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() | ||
| + 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() | ||
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| 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 | ||
| + 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 | ||
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| msPurity v0.99.0 (Release date: 2016-04-08) | ||
| ========================= | ||
| Initial release! | ||
| + Initial release! |