MSnbase v1.20.7

by Laurent Gatto

Base Functions and Classes for MS-based Proteomics

Basic plotting, data manipulation and processing of MS-based Proteomics data.

Readme

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.

Functions in MSnbase

Name Description
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
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