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

Spectra 1.3

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.

lgatto/Spectra documentation built on July 4, 2021, 5:53 p.m.

rdrr.io home R language documentation Run R code online

CRAN packages Bioconductor packages R-Forge packages GitHub packages

Note that we can't provide technical support on individual packages. You should contact the package authors for that.

Tweet to @rdrrHQ

GitHub issue tracker

ian@mutexlabs.com