NEWS

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!