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MSnbase is an R/Bioconductor package that provides infrastructure for plotting, data manipulation and processing of MS-based proteomics data. The official page is the Bioconductor landing page (release or devel versions). The github page page is for sharing, testing, issue tracking and forking/pulling purposes. Although it should be in sync with the code on the Bioconductor svn server, the latter is the official repository for the working source code.

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Version

Version

1.20.7

License

Artistic-2.0

Issues

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Stars

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Maintainer

Laurent Gatto

Last Published

February 15th, 2017

Functions in MSnbase (1.20.7)

MSnProcess-class

The "MSnProcess" Class
NAnnotatedDataFrame-class

Class Containing Measured Variables and Their Meta-Data Description for Multiplexed Experiments.
bin-methods

Bin 'MSnExp' or 'Spectrum' instances
FeaturesOfInterest-class

Features of Interest
MzTab-class

Parse MzTab files
pSet-class

Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
missing-data

Documenting missing data visualisation
MSnSetList-class

Storing multiple related MSnSets
averageMSnSet

Generate an average MSnSet
grepEcols

Returns the matching column names of indices.
smooth-methods

Smooths 'MSnExp' or 'Spectrum' instances
combineFeatures

Combines features in an MSnSet object
chromatogram-methods

Plots a chromatogram
iPQF

iPQF: iTRAQ (and TMT) Protein Quantification based on Features
extractPrecSpectra-methods

Extracts precursor-specific spectra from an 'MSnExp' object
Spectrum-class

The "Spectrum" Class
nQuants

Count the number of quantitfied features.
FeatComp-class

Class "FeatComp"
imageNA2

NA heatmap visualisation for 2 groups
compareSpectra-methods

Compare Spectra of an 'MSnExp' or 'Spectrum' instances
Spectrum2-class

The "Spectrum2" Class for MSMS Spectra
plot.Spectrum.Spectrum-methods

Plotting a 'Spectrum' vs another 'Spectrum' object.
TMT6

TMT 6-plex set
ReporterIons-class

The "ReporterIons" Class
impute-methods

Quantitative proteomics data imputation
plotMzDelta-methods

The delta m/z plot
naplot

Overview of missing value
addIdentificationData-methods

Adds Identification Data
formatRt

Format Retention Time
MSnSet-class

The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
normalise-methods

Normalisation of MSnExp, MSnSet and Spectrum objects
plot-methods

Plotting 'Spectrum' object(s)
removeNoId-methods

Removes non-identified features
npcv

Non-parametric coefficient of variation
makeNaData

Create a data with missing values
readMSData

Imports mass-spectrometry raw data files as 'MSnExp' instances.
readMzTabData_v0.9

Read an 'mzTab' file
plot2d-methods

The 'plot2d' method for 'MSnExp' quality assessment
readMzTabData

Read an 'mzTab' file
readMgfData

Import mgf files as 'MSnExp' instances.
precSelection

Number of precursor selection events
purityCorrect-methods

Performs reporter ions purity correction
selectFeatureData

Select feature variables of interest
MIAPE-class

The "MIAPE" Class for Storing Proteomics Experiment Information
commonFeatureNames

Keep only common feature names
compareMSnSets

Compare two MSnSets
itraqdata

Example MSnExp and MSnSet data sets
readMSnSet

Read 'MSnSet'
removeReporters-methods

Removes reporter ion tag peaks
MSnExp-class

The 'MSnExp' Class for MS Data And Meta-Data
Spectrum1-class

The "Spectrum1" Class for MS1 Spectra
clean-methods

Cleans 'MSnExp' or 'Spectrum' instances
calculateFragments-methods

Calculate ions produced by fragmentation.
exprsToRatios-methods

Calculate all ratio pairs
featureCV

Calculates coeffivient of variation for features
get.amino.acids

Amino acids
pickPeaks-methods

Peak Detection for 'MSnExp' or 'Spectrum' instances
iTRAQ4

iTRAQ 4-plex set
removePeaks-methods

Removes low intensity peaks
trimMz-methods

Trims 'MSnExp' or 'Spectrum' instances
xic-methods

Extracted ion chromatograms
MSmap-class

Class MSmap
estimateNoise-methods

Noise Estimation for 'Spectrum' instances
plotNA-methods

Exploring missing data in 'MSnSet' instances
get.atomic.mass

Atomic mass.
writeMgfData-methods

Write an experiment or spectrum to an mgf file
MSnbase-package

MSnbase: Base Functions and Classes for MS-based Proteomics
Deprecated

MSnbase Deprecated and Defunct
fillUp

Fills up a vector
getVariableName

Return a variable name
listOf

Tests equality of list elements class
quantify-methods

Quantifies 'MSnExp' and 'Spectrum' objects
plotDensity-methods

The 'plotDensity' method for 'MSnExp' quality assessment