- Import
extractByIndex()from ProtGenerics.
- Complete unit test coverage.
- Add new
extractByIndex()method.
compound_tbl_lipidblastsupports 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 typenumeric.
compound_tbl_lipidblast: add parameternto 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
CompDbto 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.
- Import method generics from
ProtGenerics.
- Adapt script to create CompDb from MassBank to new MassBank database format.
- Add
backendBpparamto define (disable) parallel processing for theMsBackendCompDbbackend.
- Evaluate validity of the
MsBackendCompDbusing the full test suite from theSpectrapackage.
- Add parameter
nonStoptocompound_tbl_sdfthat is passed to parameterskipErrorsofChemmineR::read.SDFset. Issue #110
- Bioconductor 3.17 developmental version.
CompDbtests also forNAinput.
MsBackendCompDbalways returnscollisionEnergyasnumeric.
- Add script to create a
CompDbfrom a MassBank database.
- Expand vignette with examples to create
CompDbdatabases from scratch.
- Add
insertCompoundanddeleteCompoundfunctions to add or remove compounds from aCompDborIonDb.
- Fix wrong warning message in
deleteIon. - Change database data type for internal
ion_idfromcharactertointeger.
- Add
mass2mzmethod forCompDbdatabases.
- Add
peaksVariablesmethod.
- Add parameter
columnstopeaksData.
- Add parameter
dbFiletocreateCompDband add an example on how to create aCompDbdatabase from custom input.
- Add citation.
- Add bug reports link to DESCRIPTION.
MsBackendCompDbextendsSpectra::MsBackendCachedinstead ofSpectra::MsBackendDataFrame.
- No updates, just version bump to cause a new build.
- Address more comments from @jianhong.
- Fix
BiocCheckwarnings.
- Fix
BiocCheckwarnings.
- Address comments/change requests from @jianhong.
- Preparing for Bioconductor submission.
- Add
deleteIonanddeleteSpectraallowing to delete ions or spectra.
insertIonssupports adding additional database columns.
- Add
instertSpectramethod to add MS/MS spectra from aSpectraobject to the database.
- Add
IonDbconstructor methods. - Expand documentation and examples.
- Add and fix unit tests.
- Add
IonDbclass as extension ofCompDb(to allow adding ion information to the database) and the functionalities to create such object. - Add
insertIonto allow adding new ions to anIonDbobject - Add
ionVariables,ionsfunctions to access the ions data in the database. - Add filters:
IonIdFilter,IonAdductFilter,IonMzFilter,IonRtFilter.
- Import spectra type (MS level) and precursor type from MoNa.
- Rename database table name compound into ms_compound issue #74.
- Remove
mass2mzandmz2massfunction in favour of the functions implemented inMetaboCoreUtils.
- Import
compoundsmethod fromProtGenerics.
- Add parameter
onlyValidtocompound_tbl_sdfto allow importing of only valid elements issue #69.
- Add additional filters:
MassFilter,FormulaFilter,InchiFilterandInchikeyFilter.
- Add
metadata,spectraVariablesandcompoundVariablesfunctions.
- Support creation of databases without specifying the organism.
- Ensure database columns are mapped correctly to Spectra variable names.
- Add
SpectrumIdFilterto support filtering by spectrum IDs.
- Rename column names: compound_name -> name, mass -> exactmass, inchi_key -> inchikey.
- Replace
as.listwithpeaksData. - Replace
asDataFramewithspectraData.
- Updated to match new LIPID MAPS field names.
- Fix bug in
as.list,MsBackendCompDbwhich returned aSimpleListinstead of alist.
- Rename method
spectraDataforMsBackendCompDbintoasDataFrame(adapting to the changes inSpectra).
- 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.
- 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.
- 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.
- 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.