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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 1.3.0
- 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
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
Changes in version 0.99.2
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.