NEWS.md
In EuracBiomedicalResearch/CompoundDb: Creating and Using (Chemical) Compound Annotation Databases

CompoundDb version 1.9

Add new extractByIndex() method.

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

compound_tbl_lipidblast: ensure exactmass is of type numeric.

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.

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

Import method generics from ProtGenerics.

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

CompoundDb version 1.3

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

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

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

Bioconductor 3.17 developmental version.

CompoundDb version 1.1

CompDb tests also for NA input.

MsBackendCompDb always returns collisionEnergy as numeric.

Add script to create a CompDb from a MassBank database.

Expand vignette with examples to create CompDb databases from scratch.

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

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

Version 0.99

Add mass2mz method for CompDb databases.

Add peaksVariables method.

Add parameter columns to peaksData.

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

Add citation.

Add bug reports link to DESCRIPTION.

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

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

Address more comments from @jianhong.

Fix BiocCheck warnings.

Fix BiocCheck warnings.

Address comments/change requests from @jianhong.

Preparing for Bioconductor submission.

Version 0.9

Add deleteIon and deleteSpectra allowing to delete ions or spectra.

insertIons supports adding additional database columns.

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

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

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

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

Rename database table name compound into ms_compound issue #74.

Version 0.7

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

Version 0.6

Import compounds method from ProtGenerics.

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

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

Add metadata, spectraVariables and compoundVariables functions.

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

Add SpectrumIdFilter to support filtering by spectrum IDs.

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

Version 0.5

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

Version 0.4

Updated to match new LIPID MAPS field names.

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

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

Version 0.3

Import also smiles from SDF files.

Move package Spectra from Depends to Imports

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

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

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.

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).

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

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

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

Add CompoundIdFilter and CompoundNameFilter classes and filtering framework.

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.

EuracBiomedicalResearch/CompoundDb documentation built on Oct. 1, 2024, 2:16 p.m.

rdrr.io home R language documentation Run R code online

CRAN packages Bioconductor packages R-Forge packages GitHub packages

Note that we can't provide technical support on individual packages. You should contact the package authors for that.

Tweet to @rdrrHQ

GitHub issue tracker

ian@mutexlabs.com