Changes in version 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.
Changes in 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.
Changes in 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
- 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.
Changes in 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.
Changes in 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
- 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.
Changes in 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.
Changes in 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.
Changes in version 0.7
Changes in version 0.7.0
- Remove mass2mz and mz2mass function in favour of the functions
implemented in MetaboCoreUtils.
Changes in 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.
Changes in version 0.5
Changes in version 0.5.0
- Replace as.list with peaksData.
- Replace asDataFrame with spectraData.
Changes in 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).
Changes in 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.
Changes in 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.
Changes in 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.
Changes in 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.