Package: rawrr 1.13.0

Christian Panse

rawrr: Direct Access to Orbitrap Data and Beyond

This package wraps the functionality of the RawFileReader .NET 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], Tobias Kockmann [aut]

rawrr_1.13.0.tar.gz
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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-1.13.0(bioc 3.20)rawrr-1.12.0(bioc 3.19)

bioconductor-package

26 exports 1.95 score 0 dependencies 2 dependents

Last updated 30 days agofrom:89daeb78c5

Exports:.checkDllInMonoPath.thermofisherlsmsUrlbasePeakbuildRawrrExedependentScanfaimsVoltageOninstallRawFileReaderDLLsinstallRawrrExeis.rawrrChromatogramis.rawrrSpectrumis.rawrrSpectrumSetmakeAccessormassRangemasterScanrawrrAssemblyPathrawrrSpectrumreadChromatogramreadFileHeaderreadIndexreadSpectrumreadTrailersampleFilePathscanNumberticvalidate_rawrrIndexvalidate_rawrrSpectrum

Dependencies:

Readme and manuals

Help Manual

Help pageTopics
Check if a file is contained in the environment variable 'MONO_PATH'..checkDllInMonoPath
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
Download and install the New RawFileReader from Thermo Fisher Scientific .Net assemblies iinstallRawFileReaderDLLs Thermo ThermoFisher ThermoFisherScientific
Download and install the 'rawrr.exe' console applicationinstallRawrrExe 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