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Changelog

Source: NEWS.md

CompoundDb version 1.11

Changes in version 1.11.1

  • Complete unit test coverage.

CompoundDb version 1.9

Changes in version 1.9.5

Changes in version 1.9.4

  • compound_tbl_lipidblast supports now parallel processing and extracts more information from MoNA’s JSON format (thanks to Prateek Arora for contribution).

Changes in version 1.9.3

  • compound_tbl_lipidblast: ensure exactmass is of type numeric.

Changes in version 1.9.2

  • compound_tbl_lipidblast: add parameter n to support reading and processing MoNA json files in sets (chunks) of lines at a time and hence reduce memory demand for very large files.

Changes in version 1.9.1

  • Allow CompDb to store that database name as alternative to an active database connection. This allows to serialize and load an object to/from disk (serializing an active database connection would not be possible) . Each call to extract data from the database will however open (and close) its own connection.

CompoundDb version 1.7

Changes in version 1.7.2

  • Import method generics from ProtGenerics.

Changes in version 1.7.1

  • Adapt script to create CompDb from MassBank to new MassBank database format.

CompoundDb version 1.3

Changes in version 1.3.3

  • Add backendBpparam to define (disable) parallel processing for the MsBackendCompDb backend.

Changes in version 1.3.2

  • Evaluate validity of the MsBackendCompDb using the full test suite from the Spectra package.

Changes in version 1.3.2

Changes in version 1.3.0

  • Bioconductor 3.17 developmental version.

CompoundDb version 1.1

Changes in version 1.1.6

  • CompDb tests also for NA input.

Changes in version 1.1.5

  • MsBackendCompDb always returns collisionEnergy as numeric.

Changes in version 1.1.4

  • Add script to create a CompDb from a MassBank database.

Changes in version 1.1.3

  • Expand vignette with examples to create CompDb databases from scratch.

Changes in version 1.1.2

  • Add insertCompound and deleteCompound functions to add or remove compounds from a CompDb or IonDb.

Changes in version 1.1.1

  • Fix wrong warning message in deleteIon.
  • Change database data type for internal ion_id from character to integer.

Version 0.99

Changes in version 0.99.12

  • Add mass2mz method for CompDb databases.

Changes in version 0.99.11

  • Add peaksVariables method.

Changes in version 0.99.10

  • Add parameter columns to peaksData.

Changes in version 0.99.9

  • Add parameter dbFile to createCompDb and add an example on how to create a CompDb database from custom input.

Changes in version 0.99.8

  • Add citation.

Changes in version 0.99.7

  • Add bug reports link to DESCRIPTION.

Changes in version 0.99.6

Changes in version 0.99.5

  • No updates, just version bump to cause a new build.

Changes in version 0.99.4

Changes in version 0.99.3

  • Fix BiocCheck warnings.

Changes in version 0.99.2

  • Fix BiocCheck warnings.

Changes in version 0.99.1

  • Address comments/change requests from @jianhong.

Changes in version 0.99.0

  • Preparing for Bioconductor submission.

Version 0.9

Changes in version 0.9.4

  • Add deleteIon and deleteSpectra allowing to delete ions or spectra.

Changes in version 0.9.3

  • insertIons supports adding additional database columns.

Changes in version 0.9.2

  • Add instertSpectra method to add MS/MS spectra from a Spectra object to the database.

Changes in version 0.9.1

  • Add IonDb constructor methods.
  • Expand documentation and examples.
  • Add and fix unit tests.

Changes in version 0.9.0

  • Add IonDb class as extension of CompDb (to allow adding ion information to the database) and the functionalities to create such object.
  • Add insertIon to allow adding new ions to an IonDb object
  • Add ionVariables, ions functions to access the ions data in the database.
  • Add filters: IonIdFilter, IonAdductFilter, IonMzFilter, IonRtFilter.

Version 0.8

Changes in version 0.8.1

  • Import spectra type (MS level) and precursor type from MoNa.

Changes in version 0.8.0

  • Rename database table name compound into ms_compound issue #74.

Version 0.7

Changes in version 0.7.0

  • Remove mass2mz and mz2mass function in favour of the functions implemented in MetaboCoreUtils.

Version 0.6

Changes in version 0.6.6

  • Import compounds method from ProtGenerics.

Changes in version 0.6.5

  • Add parameter onlyValid to compound_tbl_sdf to allow importing of only valid elements issue #69.

Changes in version 0.6.4

  • Add additional filters: MassFilter, FormulaFilter, InchiFilter and InchikeyFilter.

Changes in version 0.6.3

  • Add metadata, spectraVariables and compoundVariables functions.

Changes in version 0.6.2

  • Support creation of databases without specifying the organism.
  • Ensure database columns are mapped correctly to Spectra variable names.

Changes in version 0.6.1

  • Add SpectrumIdFilter to support filtering by spectrum IDs.

Changes in version 0.6.0

  • Rename column names: compound_name -> name, mass -> exactmass, inchi_key -> inchikey.

Version 0.5

Changes in version 0.5.0

  • Replace as.list with peaksData.
  • Replace asDataFrame with spectraData.

Version 0.4

Changes in version 0.4.3

  • Updated to match new LIPID MAPS field names.

Changes in version 0.4.2

  • Fix bug in as.list,MsBackendCompDb which returned a SimpleList instead of a list.

Changes in version 0.4.0

  • Rename method spectraData for MsBackendCompDb into asDataFrame (adapting to the changes in Spectra).

Version 0.3

Changes in version 0.3.2

  • Import also smiles from SDF files.

Changes in version 0.3.1

  • Move package Spectra from Depends to Imports

Changes in version 0.3.0

  • Change from MSnbase to RforMassSpectrometry packages (Spectra and MsCoreUtils).
  • Store MS/MS spectra in two tables, msms_spectrum and msms_spectrum_peak.

Version 0.2

Changes in version 0.2.3

  • Add instrument and precursor_mz spectra data columns (issue #32).

Changes in version 0.2.2

  • Add adduct information from Jan Stanstrup’s commonMZ package.
  • Add matchWithPpm function to match numeric values allowing for a small difference.
  • Add adducts function to retrieve adduct definitions.
  • Add mass2mz and mz2mass to convert between mass and m/z for provided adducts.
  • Add annotateMz method to annotate m/z values.

Changes in version 0.2.1

  • Change field collision_energy to character to support values from MoNa (issue #31).
  • Add functions import_mona_sdf and msms_spectra_mona functions to enable import of spectrum data from MoNa SDF files (issue #30).
  • Add support for MoNa SDF files (issue #30).

Changes in version 0.2.0

  • Add hasMz,Spectrum and hasMz,Spectra methods to look for m/z values within spectra (issue #28).
  • Add MsmsMzRangeMinFilter and MsmsMzRangeMaxFilter (issue #29).
  • Re-use Spectra object from MSnbase.
  • Add supportedFilters,CompDb method.

Version 0.1

Changes in version 0.1.1

  • Add precursorMz, precursorCharge, precursorIntensity, acquisitionNum, scanIndex, peaksCount, msLevel, tic, ionCount, collisionEnergy, fromFile, polarity, smoothed, isEmpty, centroided and isCentroided methods for Spectrum2List.

Changes in version 0.1.0

  • Add expandMzIntensity function.
  • Add spectra method to extract spectra from the CompDb database.
  • Add functionality to store MS/MS spectra in a CompDb database (m/z and intensity values stored as BLOB).
  • Add functionality to load MS/MS spectra from HMDB xml files.

Version 0.0

Changes in version 0.0.3

  • Add CompoundIdFilter and CompoundNameFilter classes and filtering framework.

Changes in version 0.0.2

  • Define CompDb class and all functionality to create CompDb databases.
  • createCompDb supports file names as input and create a database including annotations from all files.
  • Add create-compounddb vignette.