Package: rtms 0.2.0

rtms: R Toolkit for Mass Spectrometry

Quickly imports, processes, analyzes, and visualizes mass-spectrometric data. Includes functions for easily extracting specific data and measurements from large (multi-gigabyte) raw Bruker data files, as well as a set of S3 object classes for manipulating and measuring mass spectrometric peaks and plotting peaks and spectra using the 'ggplot2' package.

Authors:Mary Ashley Rimmer [aut], Nathaniel Twarog [aut, cre]

rtms_0.2.0.tar.gz
rtms_0.2.0.zip(r-4.5)rtms_0.2.0.zip(r-4.4)rtms_0.2.0.zip(r-4.3)
rtms_0.2.0.tgz(r-4.4-any)rtms_0.2.0.tgz(r-4.3-any)
rtms_0.2.0.tar.gz(r-4.5-noble)rtms_0.2.0.tar.gz(r-4.4-noble)
rtms_0.2.0.tgz(r-4.4-emscripten)rtms_0.2.0.tgz(r-4.3-emscripten)
rtms.pdf |rtms.html✨
rtms/json (API)

# Install 'rtms' in R:
install.packages('rtms', repos = c('https://nathanieltwarog.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.00 score 2 scripts 136 downloads 30 exports 28 dependencies

Last updated 1 years agofrom:7b8126d7d2. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 29 2024
R-4.5-winOKOct 29 2024
R-4.5-linuxOKOct 29 2024
R-4.4-winOKOct 29 2024
R-4.4-macOKOct 29 2024
R-4.3-winOKOct 29 2024
R-4.3-macOKOct 29 2024

Exports:closeBrukerMCFReaderemptySampleSetgetBrukerBAFAllMetadatagetBrukerBAFMetadatagetBrukerBAFSamplegetBrukerBAFSpectrumgetBrukerMCFAllMetadatagetBrukerMCFIndicesgetBrukerMCFIntensitiesgetBrukerMCFMetadatagetBrukerMCFSamplegetBrukerMCFSampleSetgetBrukerMCFSpectrumgetBrukerMCFSpotsgetSamplegetSampleFromSpectrumgetSampleSetgetSpectrummeasureSamplemeasureSampleSetnewBrukerBAFReadernewBrukerMCFReaderplotRtmsSampleplotRtmsSampleSetplotRtmsSpectrumreopenreopenBrukerMCFReaderrtmsPeakrtmsPeakListrtmsSpectrum

Dependencies:clicolorspacefansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigR6RColorBrewerrlangscalestibbleutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
Generate an empty RTMS sample setemptySampleSet
Simple Example SpectrumexampleSpectrum
Retrieve all metadata values from a Bruker BAF filegetBrukerBAFAllMetadata
Retrieve specific metadata values from a Bruker BAF filegetBrukerBAFMetadata
Retrieve all metadata values from a Bruker MCF filegetBrukerMCFAllMetadata
Retrieve peak intensities directly from an MCF filegetBrukerMCFIntensities
Retrieve specific metadata values from a Bruker BAF filegetBrukerMCFMetadata
Get spot names and indices from a Bruker MCF filegetBrukerMCFIndices getBrukerMCFSpots
Get an RTMS SamplegetSample
Extract a sample from a Bruker BAF directorygetBrukerBAFSample getSample.rtmsBrukerBAFReader
Extract a sample from a Bruker MCF directorygetBrukerMCFSample getSample.rtmsBrukerMCFReader
Extract a sample from an RTMS spectrum objectgetSample.rtmsSpectrum getSampleFromSpectrum
Get an RTMS Sample SetgetSampleSet
Extract a sample set from a Bruker MCF directorygetBrukerMCFSampleSet getSampleSet.rtmsBrukerMCFReader
Get an RTMS SpectrumgetSpectrum
Extract a spectrum from a Bruker BAF directorygetBrukerBAFSpectrum getSpectrum.rtmsBrukerBAFReader
Extract a spectrum from a Bruker MCF directorygetBrukerMCFSpectrum getSpectrum.rtmsBrukerMCFReader
Measure peaks in an RTMS samplemeasureSample
Measure peaks and samples in an RTMS sample setmeasureSampleSet
Open a Bruker single-acquisition BAF directorynewBrukerBAFReader
Open a Bruker multi-acquisition MCF directorynewBrukerMCFReader
Plot an RTMS sample objectplotRtmsSample
Plot an RTMS sample set objectplotRtmsSampleSet
Plot an RTMS spectrum objectplotRtmsSpectrum
Reopen a reader objectreopen
Manage an MCF reader file connectionclose.rtmsBrukerMCFReader closeBrukerMCFReader reopen.rtmsBrukerMCFReader reopenBrukerMCFReader
Create an RTMS m/z Peak ObjectrtmsPeak
Create a list of RTMS m/z peak objectsrtmsPeakList
Create a new RTMS spectrumrtmsSpectrum
Functions for creating and manipulating samples and sample setsrep.rtmsSample rep.rtmsSampleSet sampleAndSampleSet [.rtmsSampleSet [[.rtmsSampleSet [[<-.rtmsSampleSet