Package: rawrr 1.15.8

Christian Panse

rawrr: Direct Access to Orbitrap Data and Beyond

This package wraps the functionality of the Thermo Fisher Scientic RawFileReader .NET 8.0 assembly. Within the R environment, spectra and chromatograms are represented by S3 objects. The package provides basic functions to download and install the required third-party libraries. The package is developed, tested, and used at the Functional Genomics Center Zurich, Switzerland.

Authors:Christian Panse [aut, cre], Leonardo Schwarz [ctb], Tobias Kockmann [aut]

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rawrr.pdf |rawrr.html
rawrr/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/fgcz/rawrr/issues

On BioConductor:rawrr-1.15.0(bioc 3.21)rawrr-1.14.0(bioc 3.20)

massspectrometryproteomicsmetabolomicsinfrastructuresoftwarefastmass-spectrometrymultiplatformorbitrap-ms

8.35 score 54 stars 2 packages 23 scripts 373 downloads 24 exports 0 dependencies

Last updated 9 days agofrom:a85e4eff38. Checks:OK: 1 ERROR: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 13 2024
R-4.5-winERRORNov 13 2024
R-4.5-linuxERRORNov 13 2024
R-4.4-winERRORNov 13 2024
R-4.4-macERRORNov 13 2024
R-4.3-winERRORNov 13 2024
R-4.3-macERRORNov 13 2024

Exports:basePeakbuildRawrrExedependentScanfaimsVoltageOninstallRawFileReaderDLLsinstallRawrrExeis.rawrrChromatogramis.rawrrSpectrumis.rawrrSpectrumSetmakeAccessormassRangemasterScanrawrrAssemblyPathrawrrSpectrumreadChromatogramreadFileHeaderreadIndexreadSpectrumreadTrailersampleFilePathscanNumberticvalidate_rawrrIndexvalidate_rawrrSpectrum

Dependencies:

The rawrr R package - Direct Access to Orbitrap Data and Beyond

Rendered fromrawrr.Rmdusingknitr::rmarkdownon Nov 13 2024.

Last update: 2024-11-11
Started: 2021-02-11

Readme and manuals

Help Manual

Help pageTopics
Benchmark spectra per second.benchmark
Download and install the Thermo Fisher Scientific .NET 8.0 nupkgs.downloadNupkgs Thermo ThermoFisher ThermoFisherScientific
URL for Thermo Fisher .NET assemblies.thermofisherlsmsUrl
deriving area under the curve (AUC)auc.rawrrChromatogram
Base peak of a spectrumbasePeak
Build 'rawrr.exe' console application.buildRawrrExe
Retrieve dependent scan(s) of a scan listed in scan indexdependentScan
Is FAIMS Voltage on?faimsVoltageOn
determine scan numbers which match a specified filterfilter
deprecated installRawFileReaderDLLsinstallRawFileReaderDLLs
Download 'rawrr' assemblyinstallRawrrExe rawrr.exe
Function to check if an object is an instance of class 'rawrrChromatogram'is.rawrrChromatogram
Function to check if an object is an instance of class 'rawrrSpectrum'is.rawrrSpectrum
Function to check if an object is an instance of class 'rawrrSpectrumSet'is.rawrrSpectrumSet
Make accessor function for key value pair returned by RawFileReadermakeAccessor
Acquisition/scan range of spectrummassRange
Retrieve master scan of scan listed in scan indexmasterScan
Create instances of class 'rawrrSpectrum'new_rawrrSpectrum
Plot 'rawrrChromatogram' objectsplot.rawrrChromatogram
Plot 'rawrrChromatogramSet' objectsplot.rawrrChromatogramSet
Basic plotting function for instances of 'rawrrSpectrum'plot.rawrrSpectrum
Print method imitate the look and feel of Thermo Fisher Scientific FreeStyle's outputprint.rawrrSpectrum
Derives the path where all .NET assemblies are stored.rawrrAssemblyPath
Create 'rawrrSpectrum' objectsrawrrSpectrum
Extracts chromatographic data from a raw file.readChromatogram
read file header InformationreadFileHeader
Read scan indexreadIndex
Reads spectral data from a raw file.rawrr readSpectrum
Read and extract scan trailer from TFS raw files.readTrailer
A small file size 'sample.raw' BLOBsample.raw sampleFilePath
Accessor function for scan number of 'rawrrSpectrum' objectsscanNumber
Text summary of chromatogramsummary.rawrrChromatogram
Basic summary functionsummary.rawrrSpectrum
Total ion current of a spectrumtic
Validate output of the readIndex functionvalidate_rawrrIndex
Validate instance of class rawrrSpectrumvalidate_rawrrSpectrum