NEWS

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CompoundDb 1.9

Changes in version 1.9.5

• Add new extractByIndex() method.

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 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 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

• Add parameter nonStop to compound_tbl_sdf that is passed to parameter skipErrors of ChemmineR::read.SDFset. Issue #110

Changes in version 1.3.0

• Bioconductor 3.17 developmental version.

CompoundDb 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.

CompoundDb 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

• MsBackendCompDb extends Spectra::MsBackendCached instead of Spectra::MsBackendDataFrame.

Changes in version 0.99.5

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

Changes in version 0.99.4

• Address more comments from @jianhong.

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.

CompoundDb 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.

CompoundDb 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.

CompoundDb 0.7

Changes in version 0.7.0

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

CompoundDb 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.

CompoundDb 0.5

Changes in version 0.5.0

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

CompoundDb 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).

CompoundDb 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.

CompoundDb 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.

CompoundDb 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.

CompoundDb 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.