Changes in version 1.10 Changes in 1.10.3 - Fix issue with filterFourierTransformArtefacts function (see issue #302). Thanks Adriano Rutz for reporting. Changes in 1.10.2 - Fix setBackend,Spectra to disable parallel processing if not both backends support that. Changes in 1.10.1 - Add example for filtering precursor m/z peaks from fragment spectra to the vignette. Changes in version 1.9 Changes in 1.9.15 - Fix issue in MsBackendMemory failed to return intensity or m/z values when peaks data is empty. - Fix bug in filterPrecursorScan() (see #194 and PR #277). Changes in 1.9.14 - Fix issue with filterMzValues that would only keep (or remove) the first matching peak instead of all matching peaks (given ppm and tolerance). Issue #274. - Add parameter keep to filterMzRange to support keeping or removing matching peaks. Changes in 1.9.13 - Add the backendBpparam method that allows to evaluate whether a MsBackend supports the provided (or the default) BiocParallel-based parallel processing setup. - Minor tweaks in the internal .peaksapply function to avoid splitting/merging of data if not needed (e.g. if no parallel processing is performed). - Minor tweaks in spectra comparison functions to avoid repeated calling of functions in loops. Changes in 1.9.12 - Extend the list of available MsBackend backends provided by other packages (in the README and in the package vignette). Changes in 1.9.11 - Fix headers in MsBackend vignette. Changes in 1.9.10 - Add supportsSetBackend method for MsBackend to specify whether a backend supports setBackend,Spectra. - setBackend checks using supportsSetBackend whether a backend supports setBackend. Changes in 1.9.9 - Refactor setBackend to only split and merge backends if necessary and to not change dataOrigin of the original backend. - Support setBackend with MsBackendMemory for an empty Spectra object (issue #268). - Disable automatic detection of peak variables for MsBackendMemory (issue #269). - Fix issue in Spectra with empty character (issue #267). Changes in 1.9.8 - Address comments from Michele Stravs regarding the MsBackend vignette. - Add additional tests checking for MsBackend compliance. Changes in 1.9.7 - Add a vignette describing how to build a MsBackend from scratch (issue #262). - Extend unit test suite to evaluate validity of MsBackend implementations. Changes in 1.9.6 - Replace <= with between calls. Changes in 1.9.5 - Fix bug in containsMz() when mz isn't ordered (see #258). Changes in 1.9.4 - Fix error when extracting spectra variables from a MsBackendMzR of length 0. Changes in 1.9.3 - Add chunkapply function to split a Spectra into chunks and stepwise apply a function FUN to each. Changes in 1.9.2 - combineSpectra on Spectra with read-only backends change backend to an MsBackendMemory instead of an MsBackendDataFrame. Changes in 1.9.1 - Expand documentation on compareSpectra for GNPS-like similarity scoring. Changes in 1.9.0 - Bioconductor 3.17 developmental version. Changes in version 1.7 Changes in 1.7.5 - Force serial processing in some unit tests to avoid potential failures on some Bioconductor build and check servers (under some circumstances). Changes in 1.7.4 - Add MsBackendMemory backend class providing a more efficient in-memory data representation than MsBackendDataFrame. Changes in 1.7.3 - Import spectrapply from ProtGenerics. Changes in 1.7.2 - Fix setBackend if provided Spectra is empty. - backendInitialize,Spectra,MsBackendDataFrame returns a Spectra object with the full provided spectra data. Changes in 1.7.1 - Add uniqueMsLevels function to allow more efficient, backend-specific, implementations for retrieving unique MS levels from a data set. Changes in version 1.5 Changes in 1.5.20 - Add parameters ppm and tolerance to PrecursorMzParam (for neutral loss calculation) and add option filterPeaks = "removePrecursor". Changes in 1.5.19 - Improved the bin method. Changes in 1.5.18 - Set default for parameter columns in peaksData,Spectra and peaksData,MsBackend to c("mz", "intensity"). Changes in 1.5.17 - Add peaksVariables method and add parameter columns (or ...) to peaksData. - Add columns parameter to the peaksData method of MsBackendDataFrame, MsBackendMzR and MsBackendHdf5peaks. Changes in 1.5.16 - Fix issue in neutralLoss that would prevent calculation of neutral loss spectra if Changes in 1.5.15 - Fix typo in MZ delta plot title. Changes in 1.5.14 - Add coreSpectraVariables function to export the core spectra variables and their expected data types. Changes in 1.5.13 - Fix figure sizes in vignette. Changes in 1.5.12 - Add neutralLoss method and first algorithm to calculate neutral loss spectra. Changes in 1.5.11 - Fix neutral loss example in the vignette. Changes in 1.5.10 - Add citation. Changes in 1.5.9 - Add examples for combineSpectra to the vignette. Changes in 1.5.8 - Add spectraVariableMapping generic. Changes in 1.5.7 - Add missing export of the filterPrecursorMz method. Changes in 1.5.6 - Add filterPrecursorMzValue method which allows to filter using multiple precursor m/z values (issue #230). - Fix unit test suite. Changes in 1.5.5 - Add a testing framework allowing to run standardized unit tests for new MsBackend implementations (issue #186). Changes in 1.5.4 - Add the MsBackendCached backend. Changes in 1.5.3 - Only calculate number of peaks per spectra if the processing queue of the Spectra is not empty. Otherwise call the backend's implementation (issue MsBackendSql #31). Changes in 1.5.2 - Small documentation update (related to MsCoreUtils issue #87). - New countIdentifications() function. - Add filterFourierTransformArtefacts function to remove fast fourier artefact peaks seen on e.g. Orbitrap instruments (issue #223). Changes in 1.5.1 - Don't read header information when importing peaks matrix on macOS. Changes in version 1.3 Changes in 1.3.11 - Fix error message in setBackend (issue #217). Changes in 1.3.10 - Fix bug in plotSpectra and plotSpectraMirror that would cause an error if the number of peaks in a spectrum was 1 and labels were provided. Changes in 1.3.9 - New features: joinSpectraData() now check for duplicated keys in x (throws an error) and y (thows a warning). Changes in 1.3.8 - New features: plotMzDelta() function to M/Z delta QC (ported from MSnbase). Changes in 1.3.7 - Add fix from MSnbase (issue #170) to Spectra: on macOS require reading also the spectrum header before reading the peaks data. Changes in 1.3.6 - Documentation updates for combineSpectra and combinePeaks. Changes in 1.3.5 - filterMzValues supports also removing peaks matching specified m/z values (issue #209). Changes in 1.3.4 - Add list of additional R packages and repositories providing MsBackend backends to the vignette. Changes in 1.3.3 - Move generics for bin and compareSpectra to ProtGenerics. Changes in 1.3.2 - Add parameter f to filterPrecursorScan to fix issue #194. Changes in 1.3.1 - Add estimatePrecursorIntensity function (issue #202). Changes in version 1.1 Changes in 1.1.20 - Fix concatenating empty spectra (issue #200). Changes in 1.1.19 - New filterPrecursorCharge() method. Changes in 1.1.18 - Define plotSpectraMirror as a method. Changes in 1.1.17 - Fix issue #187. - Add function concatenateSpectra to allow concatenating Spectra objects and list of Spectra objects. Changes in 1.1.16 - Support arbitrary spectra variables to be passed to the functions provided/added with addProcessing; issue #182. Changes in 1.1.15 - Pass spectras' precursor m/z to the MAPFUN in compareSpectra; issue #171. - Add joinPeaksGnps to perform a peak matching between spectra similar to the one performed in GNPS (issue #171). Changes in 1.1.14 - Support plotting of empty spectra (issue 175). Changes in 1.1.13 - Move ProcessingStep to ProtGenerics. Changes in 1.1.12 - Fix show method for Spectra to list only the 3 most recent processing steps (issue 173). - Add processingLog function to display the log messages of all processing steps of a Spectra object. Changes in 1.1.11 - Add support for ... to pickPeaks and smooth (issue 168). Changes in 1.1.10 - Import filterIntensity from ProtGenerics. Changes in 1.1.9 - Fix label in plotSpectra. Changes in 1.1.8 - filterIntensity supports passing of additional parameters to the used filter function (issue 164). Changes in 1.1.7 - Fix bug in show,ProcessingStep (issue 162). Changes in 1.1.6 - New joinSpectraData() function. Changes in 1.1.5 - Add [[,Msbackend and [[<-,MsBackend methods (issue 149). - Add [[,Spectra and [[<-,Spectra methods. Changes in 1.1.4 - Fix issue with labelCol in plotSpectra (issue #157). Changes in 1.1.3 - Implement a generic Spectra,ANY constructor replacing Spectra,DataFrame and Spectra,character. Changes in 1.1.2 - Fix problem in export to mzML files that failed for empty spectra (issue #145) Changes in 1.1.1 - Round retention time in figure titles. - Document differences between spectrumId (spectrumID), acquisitionNum and scanIndex. Changes in 1.1.0 - New Bioc devel version Changes in version 0.99 Changes in 0.99.11 - Re-add mz and intensity as core spectra variables. Changes in 0.99.10 - Fix in spectraData<-,Spectra to avoid removing m/z and intensity values (issue #146). - Add default implementations of filter functions for MsBackend. Changes in 0.99.9 - Fix in Spectra,character constructor to ensure the backend is changed even if source inherits from backend (issue #143). Changes in 0.99.8 - combineSpectra applies data processing steps in the processing queue prior to combination (issue #140). Changes in 0.99.7 - Fix problem in dropNaSpectraVariables that would also drop m/z and intensity values for most backends (issue #138. Changes in 0.99.6 - Support intensity in filterIntensity method to be a function to enable peak intensity-based filtering of spectra (issue #126). Changes in 0.99.5 - Add filterMzRange and filterMzValues to filter spectra based on an m/z range or a list of target m/z values, respectively. Changes in 0.99.4 - Add export,MsBackendMzR to export spectra data to mzML or mzXML file(s). - Add an export,MsBackend method to allow backends to take care of data export. - Refactor export,Spectra to use the MsBackend class to export the data. - Change parameter source in Spectra,character to MsBackendMzR and set parameter backend = source. Thus by default, the import backend will also be used to store the data. Changes in 0.99.3 - Replace lapply,Spectra with spectrapply,Spectra. Changes in 0.99.2 - Replace asDataFrame,MsBackend with spectraData,MsBackend. - Replace asDataFrame<-,MsBackend with spectraData<-,MsBackend. - Replace as.list,MsBackend with peaksData,MsBackend. - Replace replaceList<-,MsBackend with peaksData<-,MsBackend. - Replace as.list,Spectra with peaksData,Spectra and add methods to coerce a Spectra to a list or SimpleList. Changes in 0.99.0 - Add reset method. - Add processing by chunk to compareSpectra.