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.