NEWS.md

In Spectra: Spectra Infrastructure for Mass Spectrometry Data

Spectra 1.0

Bioconductor release 3.12 package.

Changes in 1.0.5

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

Changes in 1.0.4

• Fix show,ProcessingStep (issue #162).

Changes in 1.0.3

• Fix issue with labelCol in plotSpectra (issue #157).
• Avoid calling par(mfrow = in plotSpectra if only a single spectrum is plotted.

Changes in 1.0.2

• Add a Spectra,ANY constructor to replace the Spectra,DataFrame and Spectra,character constructor methods.

Changes in 1.0.1

• Fix export of empty spectra with MsBackendMzR (see issue #145).

Spectra 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.

Spectra documentation built on Nov. 27, 2020, 2 a.m.