Changelog

Source: NEWS.md

MsBackendTimsTof 0.98

MsBackendTimsTof 0.98.3

• Fix connection to analysis.tdf database on case-insensitive file systems.

MsBackendTimsTof 0.98.2

• Improve/simplify the way to retrieve the required shared library from Bruker #27
• Add support for the open source library in addition to the Bruker shared library #28

MsBackendTimsTof 0.98.1

• Fix caching mechanism of the MsBackendTimsTof.
• Fix extraction of MS2-related information.
• Expand unit test coverage.

MsBackendTimsTof 0.98.0

• Extract MS2 information (precursor m/z, collision energy, isolation window etc) from the SQLite databases in the .d folder(s).

MsBackendTimsTof 0.2

MsBackendTimsTof 0.2.0

• Add extractByIndex() method and update to newer Spectra package.

MsBackendTimsTof 0.1

MsBackendTimsTof 0.1.5

• Extend vignette and run all unit tests for MsBackend instances from the Spectra package.
• Add missing methods (precScanNum, spectraNames and tic).

MsBackendTimsTof 0.1.4

• MsBackendTimsTof extends MsBackendCached to support locally change or adding new spectra variables.

MsBackendTimsTof 0.1.3

• Add dataOrigin method.

MsBackendTimsTof 0.1.2

• Add peaksVariables method.

MsBackendTimsTof 0.1.1

• Disable opentimsr parallel processing to not interfere with BiocParallel (issue #16).

MsBackendTimsTof 0.1.0

• Import coreSpectraVariables from Spectra and thus depend on Spectra version >= 1.5.14.
• Return inv_ion_mobility as a spectraVariable.

MsBackendTimsTof 0.0

MsBackendTimsTof 0.0.8

• Add documentation and vignette.

MsBackendTimsTof 0.0.7

• Added msLevel to extract MS level of each spectrum in MsBackendTimsTof objects.

MsBackendTimsTof 0.0.6

• Fix issue in spectraData when parameter columns of length 1 is provided (issue [#7] (https://github.com/rformassspectrometry/MsBackendTimsTof/issues/7)).

MsBackendTimsTof 0.0.5

• Add test data.
• Add show method.
• Fix issue in peaksData with duplicated spectra (e.g. due to sps[c(1, 1, 1)]).

MsBackendTimsTof 0.0.4

• Fixed a problem in mz, intensity, peaksData methods that caused these methods to return spectra values in wrong order given a reordered MsBackendTimsTof object.
• spectraVariables and spectraData methods.
• Fixed a problem in file indexing possibly arising after object subsetting.
• Unit tests update.

MsBackendTimsTof 0.0.3

• Export MsBackendTimsTof function.
• Refactor extraction of general spectra variables.

MsBackendTimsTof 0.0.2

• mz, intensity, peaksData methods to access m/z, intensities, peak matrices of spectra in the backend.
• rtime method to access retention time of spectra in the backend.

MsBackendTimsTof 0.0.1

• MsBackendTimsTof class definition.
• backendInitialize method to initialize a MsBackendTimsTof backend.
• [ method to subset the backend object.
• length method to get object length (number of spectra in the backend)
• dataStorage method to get the TimsTOF ’*.d’ folders where each spectra is retrieved from.