NEWS.md
In rformassspectrometry/Spectra: Spectra Infrastructure for Mass Spectrometry Data

Spectra 1.17

Import extractByIndex() from ProtGenerics.

Fix cbind2() unit test for backends that fails if the number of spectra in the tested backend is (by chance) equal to 4.

Add cbind2() method to easily add multiple spectraVariables and their content to the spectraData of a Spectra object. See also issue #342

Refactor containsMz() to support chunk-wise processing.

Spectra 1.15

Add precursorMz<- method issue #336.

Add generic backendRequiredSpectraVariables() to allow definition of mandatory spectra variables for a backend.

Add reference to MsBackendMetaboLights.

Add new extractSpectra() generic and implementation for MsBackend. Fixes issue #5.

Restructure and reorganize documentation for Spectra.

Refactor the Spectra() constructor method: better support for initialization of backends that define their own specific parameters.

Change estimatePrecursorIntensity() to a method to avoid overrides/clashes with the same-named implementation in xcms.

Fix in selectSpectraVariables() for MsBackendMzR: ensure peaks variables "mz" and "intensity" are not by default removed.

Add new filterPeaksRanges() function to filter mass peaks by ranges on numeric spectra or peak variables.

For evaluation of the Spectra's processing queue: call functions from the MetaboCoreUtils directly through their namespace (MsCoreUtils::) to avoid errors if performed in parallel on Windows machines or if called on a re-loaded object.
New asDataFrame() function to convert a (small) Spectra object into a long DataFrame.

Add dataStorageDataPath() and dataStorageDataPath<- methods to allow updating/adapting the path of the data storage files of backends supporting that issue #321.

Improve documentation for combineSpectra() and combinePeaks() issue #320.

Spectra 1.13

Add estimatePrecursorMz() function to estimate the precursor m/z for DDA fragment spectra from previous MS1 spectra issue #315.

Move generics backendBpparam(), backendParallelFactor() and supportsSetBackend() to ProtGenerics. Required ProtGenerics version 1.35.4 or higher.

Add filterRanges() and filterValues() functions to allow filtering of a Spectra object based on ranges or similarities of any existing spectraData variables.

Move generics to ProtGenerics. Requires ProtGenerics version 1.35.3.

Add entropy and nentropy functions to allow to calculate the (normalized) entropy for each spectrum.

Fix issue in setBackend that might cause chunk-wise processing to be not run.

Add possibility to enable and perform chunk-wise (parallel) processing to Spectra: add functions processingChunkSize, backendParallelFactor and processingChunkFactor to set or get definition of chunks for parallel processing. All functions working on peaks data use this mechanism which is implemented in the internal .peaksapply function. The Spectra object gains a new slot "processingChunkSize" that is used to define the size of the processing chunks for the Spectra. See also issue #304. This ensures processing also of very large data sets.

Fix issue with bin function (see issue #302). Addition of zero.rm parameter to prevent creation of empty bins.

Spectra 1.11

Fix issue with filterFourierTransformArtefacts function (see issue #302). Thanks Adriano Rutz for reporting.

peaksData,MsBackendMemory returns a data.frame if additional peak variables (in addition to "mz" and "intensity") are requested. For columns = c("mz", "intensity") (the default) a list of matrix is returned.
peaksData,Spectra returns either a matrix or data.frame and ensures the peak data is correctly subset based on the lazy evaluation processing queue.
$,Spectra to access peak variables ensures the lazy evaluation queue is applied prior to extracting the values.
applyProcessing correctly subsets and processes all peak variables depending on the processing queue.
spectraData<-,Spectra throws an error if processing queue is not empty and values for peaks variables should be replaced.
$<-,Spectra throws an error if processing queue is not empty and a peaks variable is going to be replaced.
Add full support for additional peaks variables to MsBackendDataFrame.

Add filterPrecursorPeaks to allow filtering peaks within each spectrum with m/z values relative to the precursor m/z of the spectrum.

Add an example to the vignette describing how spectral similarity scores from the msentropy package can be used with compareSpectra.

Fix in compareSpectra to also pass parameters ppm and tolerance to the peak similarity calculation functions FUN: this allows to use custom similarity function with integrated mapping of peaks.
Add joinPeaksNone to skip the peak matching in compareSpectra if the similarity scoring function performs its own peak matching.
Only use parallel processing in setBackend,Spectra if both backends support it.

Add filterPrecursorMaxIntensity function.
Add filterPrecursorIsotopes function.

Add scalePeaks function (see issue #291).

Import uniqueMsLevels from ProtGenerics.

Rename combinePeaks for lists of peak matrices into combinePeaksData.
Add combinePeaks generics.
Add combinePeaks,Spectra to combine peaks within each spectrum in a Spectra.

Add deisotopeSpectra and reduceSpectra functions.

Add example for filtering precursor m/z peaks from fragment spectra to the vignette.

Spectra 1.9

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).

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.

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.

Extend the list of available MsBackend backends provided by other packages (in the README and in the package vignette).

Fix headers in MsBackend vignette.

Add supportsSetBackend method for MsBackend to specify whether a backend supports setBackend,Spectra.
setBackend checks using supportsSetBackend whether a backend supports setBackend.

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).

Address comments from Michele Stravs regarding the MsBackend vignette.
Add additional tests checking for MsBackend compliance.

Add a vignette describing how to build a MsBackend from scratch (issue #262).
Extend unit test suite to evaluate validity of MsBackend implementations.

Replace <= with between calls.

Fix bug in containsMz() when mz isn't ordered (see #258).

Fix error when extracting spectra variables from a MsBackendMzR of length 0.

Add chunkapply function to split a Spectra into chunks and stepwise apply a function FUN to each.

combineSpectra on Spectra with read-only backends change backend to an MsBackendMemory instead of an MsBackendDataFrame.

Expand documentation on compareSpectra for GNPS-like similarity scoring.

Bioconductor 3.17 developmental version.

Spectra 1.7

Force serial processing in some unit tests to avoid potential failures on some Bioconductor build and check servers (under some circumstances).

Add MsBackendMemory backend class providing a more efficient in-memory data representation than MsBackendDataFrame.

Import spectrapply from ProtGenerics.

Fix setBackend if provided Spectra is empty.
backendInitialize,Spectra,MsBackendDataFrame returns a Spectra object with the full provided spectra data.

Add uniqueMsLevels function to allow more efficient, backend-specific, implementations for retrieving unique MS levels from a data set.

Spectra 1.5

Add parameters ppm and tolerance to PrecursorMzParam (for neutral loss calculation) and add option filterPeaks = "removePrecursor".

Improved the bin method.

Set default for parameter columns in peaksData,Spectra and peaksData,MsBackend to c("mz", "intensity").

Add peaksVariables method and add parameter columns (or ...) to peaksData.
Add columns parameter to the peaksData method of MsBackendDataFrame, MsBackendMzR and MsBackendHdf5peaks.

Fix issue in neutralLoss that would prevent calculation of neutral loss spectra if

Fix typo in MZ delta plot title.

Add coreSpectraVariables function to export the core spectra variables and their expected data types.

Fix figure sizes in vignette.

Add neutralLoss method and first algorithm to calculate neutral loss spectra.

Fix neutral loss example in the vignette.

Add citation.

Add examples for combineSpectra to the vignette.

Add spectraVariableMapping generic.

Add missing export of the filterPrecursorMz method.

Add filterPrecursorMzValue method which allows to filter using multiple precursor m/z values (issue #230).
Fix unit test suite.

Add a testing framework allowing to run standardized unit tests for new MsBackend implementations (issue #186).

Add the MsBackendCached backend.

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).

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).

Don't read header information when importing peaks matrix on macOS.

Spectra 1.3

Fix error message in setBackend (issue #217).

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.

New features: joinSpectraData() now check for duplicated keys in x (throws an error) and y (thows a warning).

New features: plotMzDelta() function to M/Z delta QC (ported from MSnbase).

Add fix from MSnbase (issue #170) to Spectra: on macOS require reading also the spectrum header before reading the peaks data.

Documentation updates for combineSpectra and combinePeaks.

filterMzValues supports also removing peaks matching specified m/z values (issue #209).

Add list of additional R packages and repositories providing MsBackend backends to the vignette.

Move generics for bin and compareSpectra to ProtGenerics.

Add parameter f to filterPrecursorScan to fix issue #194.

Add estimatePrecursorIntensity function (issue #202).

Spectra 1.1

Fix concatenating empty spectra (issue #200).

New filterPrecursorCharge() method.

Define plotSpectraMirror as a method.

Fix issue #187.
Add function concatenateSpectra to allow concatenating Spectra objects and list of Spectra objects.

Support arbitrary spectra variables to be passed to the functions provided/added with addProcessing; issue #182.

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).

Support plotting of empty spectra (issue 175).

Move ProcessingStep to ProtGenerics.

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.

Add support for ... to pickPeaks and smooth (issue 168).

Import filterIntensity from ProtGenerics.

Fix label in plotSpectra.

filterIntensity supports passing of additional parameters to the used filter function (issue 164).

Fix bug in show,ProcessingStep (issue 162).

New joinSpectraData() function.

Add [[,Msbackend and [[<-,MsBackend methods (issue 149).
Add [[,Spectra and [[<-,Spectra methods.

Fix issue with labelCol in plotSpectra (issue #157).

Implement a generic Spectra,ANY constructor replacing Spectra,DataFrame and Spectra,character.

Fix problem in export to mzML files that failed for empty spectra (issue #145)

Round retention time in figure titles.
Document differences between spectrumId (spectrumID), acquisitionNum and scanIndex.

New Bioc devel version

Spectra 0.99

Re-add mz and intensity as core spectra variables.

Fix in spectraData<-,Spectra to avoid removing m/z and intensity values (issue #146).
Add default implementations of filter functions for MsBackend.

Fix in Spectra,character constructor to ensure the backend is changed even if source inherits from backend (issue #143).

combineSpectra applies data processing steps in the processing queue prior to combination (issue #140).

Fix problem in dropNaSpectraVariables that would also drop m/z and intensity values for most backends (issue #138.

Support intensity in filterIntensity method to be a function to enable peak intensity-based filtering of spectra (issue #126).

Add filterMzRange and filterMzValues to filter spectra based on an m/z range or a list of target m/z values, respectively.

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.

Replace lapply,Spectra with spectrapply,Spectra.

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.

Add reset method.
Add processing by chunk to compareSpectra.

rformassspectrometry/Spectra documentation built on Dec. 19, 2024, 1:05 p.m.

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rformassspectrometry/Spectra Spectra Infrastructure for Mass Spectrometry Data

NEWS.md In rformassspectrometry/Spectra: Spectra Infrastructure for Mass Spectrometry Data

Spectra 1.17

Change in 1.17.4

Change in 1.17.3

Change in 1.17.2

Changes in 1.17.1

Spectra 1.15

Changes in 1.15.13

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Spectra 1.13

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Spectra 1.11

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Spectra 1.9

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Spectra 1.7

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Spectra 1.5

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rformassspectrometry/Spectra
Spectra Infrastructure for Mass Spectrometry Data

NEWS.md
In rformassspectrometry/Spectra: Spectra Infrastructure for Mass Spectrometry Data