Package: rawrr 1.21.0

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]

rawrr_1.21.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
rawrr/json (API)

# Install 'rawrr' in R:

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

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

On BioConductor:rawrr-1.21.0(bioc 3.24)rawrr-1.20.0(bioc 3.23)

massspectrometry proteomics metabolomics infrastructure software fast mass-spectrometry multiplatform orbitrap-ms

8.54 score 62 stars 3 packages 41 scripts 26 exports 0 dependencies

Last updated from:7cb330161e. Checks:1 WARNING, 7 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	159
linux-devel-x86_64	ERROR	155
source / vignettes	OK	239
linux-release-x86_64	ERROR	174
macos-release-arm64	ERROR	144
macos-oldrel-arm64	ERROR	92
windows-devel	ERROR	86
windows-release	ERROR	83
windows-oldrel	ERROR	101
wasm-release	OK	119

Exports:.isAssemblyWorking .rawrrAssembly basePeak buildRawrrExe dependentScan faimsVoltageOn installRawFileReaderDLLs installRawrrExe is.rawrrChromatogram is.rawrrSpectrum is.rawrrSpectrumSet makeAccessor massRange masterScan rawrrAssemblyPath rawrrSpectrum readChromatogram readFileHeader readIndex readSpectrum readTrailer sampleFilePath scanNumber tic validate_rawrrIndex validate_rawrrSpectrum

Dependencies:

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

Rendered fromrawrr.Rmdusingknitr::rmarkdown

Last update: 2025-05-30
Started: 2021-02-11

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
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 spectrum	basePeak
Build 'rawrr.exe' console application.	buildRawrrExe
Retrieve dependent scan(s) of a scan listed in scan index	dependentScan
Is FAIMS Voltage on?	faimsVoltageOn
determine scan numbers which match a specified filter	filter
installRawFileReaderDLLs (deprecated)	installRawFileReaderDLLs
Download 'rawrr' assembly	installRawrrExe 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 RawFileReader	makeAccessor
Acquisition/scan range of spectrum	massRange
Retrieve master scan of scan listed in scan index	masterScan
Create instances of class 'rawrrSpectrum'	new_rawrrSpectrum
Plot 'rawrrChromatogram' objects	plot.rawrrChromatogram
Plot 'rawrrChromatogramSet' objects	plot.rawrrChromatogramSet
Basic plotting function for instances of 'rawrrSpectrum'	plot.rawrrSpectrum
Print method imitate the look and feel of Thermo Fisher Scientific FreeStyle's output	print.rawrrSpectrum
Derives the path where all .NET assemblies are stored.	rawrrAssemblyPath
Create 'rawrrSpectrum' objects	rawrrSpectrum
Extracts chromatographic data from a raw file.	readChromatogram
read file header Information	readFileHeader
Read scan index	readIndex
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' BLOB	sample.raw sampleFilePath
Accessor function for scan number of 'rawrrSpectrum' objects	scanNumber
Text summary of chromatogram	summary.rawrrChromatogram
Basic summary function	summary.rawrrSpectrum
Total ion current of a spectrum	tic
Validate output of the readIndex function	validate_rawrrIndex
Validate instance of class rawrrSpectrum	validate_rawrrSpectrum