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rtms (version 0.2.0)

R Toolkit for Mass Spectrometry

Description

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.

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Version

Install

install.packages('rtms')

Monthly Downloads

152

Version

0.2.0

License

GPL (>= 3)

Maintainer

Nathaniel Twarog

Last Published

June 6th, 2023

Functions in rtms (0.2.0)

getBrukerBAFMetadata

Retrieve specific metadata values from a Bruker BAF file
measureSampleSet

Measure peaks and samples in an RTMS sample set
emptySampleSet

Generate an empty RTMS sample set
reopen.rtmsBrukerMCFReader

Manage an MCF reader file connection
getSpectrum.rtmsBrukerMCFReader

Extract a spectrum from a Bruker MCF directory
sampleAndSampleSet

Functions for creating and manipulating samples and sample sets
getBrukerMCFAllMetadata

Retrieve all metadata values from a Bruker MCF file
measureSample

Measure peaks in an RTMS sample
rtmsSpectrum

Create a new RTMS spectrum
getSample.rtmsBrukerMCFReader

Extract a sample from a Bruker MCF directory
getSampleSet.rtmsBrukerMCFReader

Extract a sample set from a Bruker MCF directory
getSpectrum.rtmsBrukerBAFReader

Extract a spectrum from a Bruker BAF directory
getBrukerMCFSpots

Get spot names and indices from a Bruker MCF file
getSampleSet

Get an RTMS Sample Set
getBrukerBAFAllMetadata

Retrieve all metadata values from a Bruker BAF file
getBrukerMCFIntensities

Retrieve peak intensities directly from an MCF file
exampleSpectrum

Simple Example Spectrum
getSpectrum

Get an RTMS Spectrum
plotRtmsSample

Plot an RTMS sample object
plotRtmsSampleSet

Plot an RTMS sample set object
newBrukerBAFReader

Open a Bruker single-acquisition BAF directory
newBrukerMCFReader

Open a Bruker multi-acquisition MCF directory
getSample.rtmsSpectrum

Extract a sample from an RTMS spectrum object
getBrukerMCFMetadata

Retrieve specific metadata values from a Bruker BAF file
getSample

Get an RTMS Sample
plotRtmsSpectrum

Plot an RTMS spectrum object
reopen

Reopen a reader object
rtmsPeak

Create an RTMS m/z Peak Object
rtmsPeakList

Create a list of RTMS m/z peak objects
getSample.rtmsBrukerBAFReader

Extract a sample from a Bruker BAF directory