MSnbase: Base Functions and Classes for MS-based Proteomics

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

Author
Laurent Gatto <lg390@cam.ac.uk> with contributions from Guangchuang Yu, Samuel Wieczorek, Vasile-Cosmin Lazar, Vladislav Petyuk, Thomas Naake, Richie Cotton, Martina Fisher, Johannes Rainer and Sebastian Gibb.
Date of publication
None
Maintainer
Laurent Gatto <lg390@cam.ac.uk>
License
Artistic-2.0
Version
2.0.1
URLs

View on Bioconductor

Man pages

addIdentificationData-methods
Adds Identification Data
averageMSnSet
Generate an average 'MSnSet'
bin-methods
Bin 'MSnExp' or 'Spectrum' instances
calculateFragments-methods
Calculate ions produced by fragmentation.
chromatogram-methods
Plots a chromatogram
clean-methods
Cleans 'MSnExp' or 'Spectrum' instances
combineFeatures
Combines features in an 'MSnSet' object
commonFeatureNames
Keep only common feature names
compareMSnSets
Compare two MSnSets
compareSpectra-methods
Compare Spectra of an 'MSnExp' or 'Spectrum' instances
defunct
MSnbase Deprecated and Defunct
estimateNoise-method
Noise Estimation for 'Spectrum' instances
exprsToRatios-methods
Calculate all ratio pairs
extractPrecSpectra-methods
Extracts precursor-specific spectra from an 'MSnExp' object
FeatComp-class
Class '"FeatComp"'
featureCV
Calculates coeffivient of variation for features
FeaturesOfInterest-class
Features of Interest
fillUp
Fills up a vector
formatRt
Format Retention Time
get.amino.acids
Amino acids
get.atomic.mass
Atomic mass.
getVariableName
Return a variable name
grepEcols
Returns the matching column names of indices.
imageNA2
NA heatmap visualisation for 2 groups
impute-methods
Quantitative proteomics data imputation
iPQF
iPQF: iTRAQ (and TMT) Protein Quantification based on...
iTRAQ4
iTRAQ 4-plex set
itraqdata
Example 'MSnExp' and 'MSnSet' data sets
listOf
Tests equality of list elements class
makeNaData
Create a data with missing values
MIAPE-class
The "MIAPE" Class for Storing Proteomics Experiment...
missing-data
Documenting missing data visualisation
MSmap-class
Class 'MSmap'
MSnbaseOptions
MSnbase options
MSnbase-package
MSnbase: Base Functions and Classes for MS-based Proteomics
MSnExp-class
The 'MSnExp' Class for MS Data And Meta-Data
MSnProcess-class
The "MSnProcess" Class
MSnSet-class
The "MSnSet" Class for MS Proteomics Expression Data and...
MSnSetList-class
Storing multiple related MSnSets
MzTab-class
Parse 'MzTab' files
NAnnotatedDataFrame-class
Class Containing Measured Variables and Their Meta-Data...
naplot
Overview of missing value
normalise-methods
Normalisation of 'MSnExp', 'MSnSet' and 'Spectrum' objects
npcv
Non-parametric coefficient of variation
nQuants
Count the number of quantitfied features.
OnDiskMSnExp-class
The 'OnDiskMSnExp' Class for MS Data And Meta-Data
pickPeaks-method
Peak Detection for 'MSnExp' or 'Spectrum' instances
plot2d-methods
The 'plot2d' method for 'MSnExp' quality assessment
plotDensity-methods
The 'plotDensity' method for 'MSnExp' quality assessment
plot-methods
Plotting 'Spectrum' object(s)
plotMzDelta-methods
The delta m/z plot
plotNA-methods
Exploring missing data in 'MSnSet' instances
plotSpectrumSpectrum-methods
Plotting a 'Spectrum' vs another 'Spectrum' object.
precSelection
Number of precursor selection events
ProcessingStep-class
Simple processing step class
pSet-class
Class to Contain Raw Mass-Spectrometry Assays and...
purityCorrect-methods
Performs reporter ions purity correction
quantify-methods
Quantifies 'MSnExp' and 'Spectrum' objects
readMgfData
Import mgf files as 'MSnExp' instances.
readMSData
Imports mass-spectrometry raw data files as 'MSnExp'...
readMSnSet
Read 'MSnSet'
readMzTabData
Read an 'mzTab' file
readMzTabData_v0.9
Read an 'mzTab' file
removeNoId-methods
Removes non-identified features
removePeaks-methods
Removes low intensity peaks
removeReporters-methods
Removes reporter ion tag peaks
ReporterIons-class
The "ReporterIons" Class
selectFeatureData
Select feature variables of interest
smooth-methods
Smooths 'MSnExp' or 'Spectrum' instances
Spectrum1-class
The "Spectrum1" Class for MS1 Spectra
Spectrum2-class
The "Spectrum2" Class for MSn Spectra
Spectrum-class
The "Spectrum" Class
TMT6
TMT 6/10-plex sets
trimMz-methods
Trims 'MSnExp' or 'Spectrum' instances
updateObject-methods
Update MSnbase objects
writeMgfData-methods
Write an experiment or spectrum to an mgf file
xic-methods
Extracted ion chromatograms

Files in this package

MSnbase/.Rinstignore
MSnbase/CONDUCT.md
MSnbase/DESCRIPTION
MSnbase/NAMESPACE
MSnbase/NEWS
MSnbase/R
MSnbase/R/AllClassUnions.R
MSnbase/R/AllGenerics.R
MSnbase/R/DataClasses.R
MSnbase/R/MzTab.R
MSnbase/R/RcppExports.R
MSnbase/R/TMT10.R
MSnbase/R/TMT6.R
MSnbase/R/TMT7.R
MSnbase/R/averageMSnSet.R
MSnbase/R/cache.R
MSnbase/R/combineFeatures.R
MSnbase/R/compfnames.R
MSnbase/R/environment.R
MSnbase/R/foi.R
MSnbase/R/functions-MIAPE.R
MSnbase/R/functions-MSnExp.R
MSnbase/R/functions-MSnProcess.R
MSnbase/R/functions-MSnSet.R
MSnbase/R/functions-OnDiskMSnExp.R
MSnbase/R/functions-ReporterIons.R
MSnbase/R/functions-Spectrum.R
MSnbase/R/functions-Spectrum1.R
MSnbase/R/functions-Spectrum2.R
MSnbase/R/functions-fragments.R
MSnbase/R/functions-mzR.R
MSnbase/R/header.R
MSnbase/R/hmap.R
MSnbase/R/iPQF.R
MSnbase/R/iTRAQ4.R
MSnbase/R/iTRAQ5.R
MSnbase/R/iTRAQ8.R
MSnbase/R/iTRAQ9.R
MSnbase/R/imputation.R
MSnbase/R/map.R
MSnbase/R/matching.R
MSnbase/R/methods-MIAPE.R
MSnbase/R/methods-MSnExp.R
MSnbase/R/methods-MSnProcess.R
MSnbase/R/methods-MSnSet.R
MSnbase/R/methods-MSnSetList.R
MSnbase/R/methods-NAnnotatedDataFrame.R
MSnbase/R/methods-OnDiskMSnExp.R
MSnbase/R/methods-ProcessingStep.R
MSnbase/R/methods-ReporterIons.R
MSnbase/R/methods-Spectrum.R
MSnbase/R/methods-Spectrum1.R
MSnbase/R/methods-Spectrum2.R
MSnbase/R/methods-all.equal.R
MSnbase/R/methods-filters.R
MSnbase/R/methods-fragments.R
MSnbase/R/methods-mzR.R
MSnbase/R/methods-other.R
MSnbase/R/methods-pSet.R
MSnbase/R/methods-updateObjectTo.R
MSnbase/R/missing-data.R
MSnbase/R/nadata.R
MSnbase/R/options.R
MSnbase/R/plotting-MSnExp.R
MSnbase/R/plotting-MSnSet.R
MSnbase/R/plotting-OnDiskMSnExp.R
MSnbase/R/plotting-Spectrum.R
MSnbase/R/plotting-Spectrum1.R
MSnbase/R/plotting-Spectrum2.R
MSnbase/R/plotting-dataframe.R
MSnbase/R/quantitation-MS2-isobaric.R
MSnbase/R/quantitation-MS2-labelfree.R
MSnbase/R/readMSData.R
MSnbase/R/readMSData2.R
MSnbase/R/readMSnSet.R
MSnbase/R/readMzXMLData.R
MSnbase/R/readWriteMgfData.R
MSnbase/R/readWriteMzTab.R
MSnbase/R/utils.R
MSnbase/R/zzz.R
MSnbase/README.Rmd
MSnbase/README.md
MSnbase/build
MSnbase/build/vignette.rds
MSnbase/data
MSnbase/data/TMT10.RData
MSnbase/data/TMT10ETD.RData
MSnbase/data/TMT10HCD.RData
MSnbase/data/TMT6.RData
MSnbase/data/TMT6b.RData
MSnbase/data/TMT7.RData
MSnbase/data/TMT7b.RData
MSnbase/data/iTRAQ4.RData
MSnbase/data/iTRAQ5.RData
MSnbase/data/iTRAQ8.RData
MSnbase/data/iTRAQ9.RData
MSnbase/data/itraqdata.RData
MSnbase/data/msnset.rda
MSnbase/data/msnset2.rda
MSnbase/data/naset.rda
MSnbase/inst
MSnbase/inst/CITATION
MSnbase/inst/doc
MSnbase/inst/doc/MSnbase-demo
MSnbase/inst/doc/MSnbase-demo.R
MSnbase/inst/doc/MSnbase-demo.Rnw
MSnbase/inst/doc/MSnbase-demo.pdf
MSnbase/inst/doc/MSnbase-development
MSnbase/inst/doc/MSnbase-development.R
MSnbase/inst/doc/MSnbase-development.Rnw
MSnbase/inst/doc/MSnbase-development.pdf
MSnbase/inst/doc/MSnbase-io
MSnbase/inst/doc/MSnbase-io.R
MSnbase/inst/doc/MSnbase-io.Rnw
MSnbase/inst/doc/MSnbase-io.pdf
MSnbase/inst/doc/benchmarking.R
MSnbase/inst/doc/benchmarking.Rmd
MSnbase/inst/doc/benchmarking.html
MSnbase/inst/extdata
MSnbase/inst/extdata/M.rda
MSnbase/inst/extdata/M2.rda
MSnbase/inst/extdata/TMT6plexPurityCorrections.csv
MSnbase/inst/extdata/dummyiTRAQ.mzXML
MSnbase/inst/extdata/dummyiTRAQ.mzid
MSnbase/inst/extdata/iTRAQ4plexPurityCorrections.csv
MSnbase/inst/extdata/iTRAQ8plexPurityCorrections.csv
MSnbase/inst/extdata/ipqfres.rda
MSnbase/inst/extdata/msx.rda
MSnbase/inst/extdata/msx0.rda
MSnbase/inst/extdata/test.mgf
MSnbase/inst/scripts
MSnbase/inst/scripts/benchmarking.R
MSnbase/inst/scripts/make_msx.R
MSnbase/inst/scripts/naset.R
MSnbase/inst/scripts/torture.R
MSnbase/inst/tests
MSnbase/man
MSnbase/man/FeatComp-class.Rd
MSnbase/man/FeaturesOfInterest-class.Rd
MSnbase/man/MIAPE-class.Rd
MSnbase/man/MSmap-class.Rd
MSnbase/man/MSnExp-class.Rd
MSnbase/man/MSnProcess-class.Rd
MSnbase/man/MSnSet-class.Rd
MSnbase/man/MSnSetList-class.Rd
MSnbase/man/MSnbase-package.Rd
MSnbase/man/MSnbaseOptions.Rd
MSnbase/man/MzTab-class.Rd
MSnbase/man/NAnnotatedDataFrame-class.Rd
MSnbase/man/OnDiskMSnExp-class.Rd
MSnbase/man/ProcessingStep-class.Rd
MSnbase/man/ReporterIons-class.Rd
MSnbase/man/Spectrum-class.Rd
MSnbase/man/Spectrum1-class.Rd
MSnbase/man/Spectrum2-class.Rd
MSnbase/man/TMT6.Rd
MSnbase/man/addIdentificationData-methods.Rd
MSnbase/man/averageMSnSet.Rd
MSnbase/man/bin-methods.Rd
MSnbase/man/calculateFragments-methods.Rd
MSnbase/man/chromatogram-methods.Rd
MSnbase/man/clean-methods.Rd
MSnbase/man/combineFeatures.Rd
MSnbase/man/commonFeatureNames.Rd
MSnbase/man/compareMSnSets.Rd
MSnbase/man/compareSpectra-methods.Rd
MSnbase/man/defunct.Rd
MSnbase/man/estimateNoise-method.Rd
MSnbase/man/exprsToRatios-methods.Rd
MSnbase/man/extractPrecSpectra-methods.Rd
MSnbase/man/featureCV.Rd
MSnbase/man/fillUp.Rd
MSnbase/man/formatRt.Rd
MSnbase/man/get.amino.acids.Rd
MSnbase/man/get.atomic.mass.Rd
MSnbase/man/getVariableName.Rd
MSnbase/man/grepEcols.Rd
MSnbase/man/iPQF.Rd
MSnbase/man/iTRAQ4.Rd
MSnbase/man/imageNA2.Rd
MSnbase/man/impute-methods.Rd
MSnbase/man/itraqdata.Rd
MSnbase/man/listOf.Rd
MSnbase/man/makeNaData.Rd
MSnbase/man/missing-data.Rd
MSnbase/man/nQuants.Rd
MSnbase/man/naplot.Rd
MSnbase/man/normalise-methods.Rd
MSnbase/man/npcv.Rd
MSnbase/man/pSet-class.Rd
MSnbase/man/pickPeaks-method.Rd
MSnbase/man/plot-methods.Rd
MSnbase/man/plot2d-methods.Rd
MSnbase/man/plotDensity-methods.Rd
MSnbase/man/plotMzDelta-methods.Rd
MSnbase/man/plotNA-methods.Rd
MSnbase/man/plotSpectrumSpectrum-methods.Rd
MSnbase/man/precSelection.Rd
MSnbase/man/purityCorrect-methods.Rd
MSnbase/man/quantify-methods.Rd
MSnbase/man/readMSData.Rd
MSnbase/man/readMSnSet.Rd
MSnbase/man/readMgfData.Rd
MSnbase/man/readMzTabData.Rd
MSnbase/man/readMzTabData_v0.9.Rd
MSnbase/man/removeNoId-methods.Rd
MSnbase/man/removePeaks-methods.Rd
MSnbase/man/removeReporters-methods.Rd
MSnbase/man/selectFeatureData.Rd
MSnbase/man/smooth-methods.Rd
MSnbase/man/trimMz-methods.Rd
MSnbase/man/updateObject-methods.Rd
MSnbase/man/writeMgfData-methods.Rd
MSnbase/man/xic-methods.Rd
MSnbase/src
MSnbase/src/MSnbase.h
MSnbase/src/RcppExports.cpp
MSnbase/src/Spectrum1_class.c
MSnbase/src/Spectrum2_class.c
MSnbase/src/imp_neighbour_avg.cpp
MSnbase/src/utils.c
MSnbase/tests
MSnbase/tests/testthat
MSnbase/tests/testthat.R
MSnbase/tests/testthat/dont_test_plotMzDelata.R
MSnbase/tests/testthat/test_MIAPE.R
MSnbase/tests/testthat/test_MSmap.R
MSnbase/tests/testthat/test_MSnExp.R
MSnbase/tests/testthat/test_MSnExpFilters.R
MSnbase/tests/testthat/test_MSnExpSubsetting.R
MSnbase/tests/testthat/test_MSnProcess.R
MSnbase/tests/testthat/test_MSnSet.R
MSnbase/tests/testthat/test_MzTab.R
MSnbase/tests/testthat/test_MzTab_09.R
MSnbase/tests/testthat/test_NAnnotatedDataFrame.R
MSnbase/tests/testthat/test_OnDiskMSnExp.R
MSnbase/tests/testthat/test_OnDiskMSnExp2.R
MSnbase/tests/testthat/test_OnDiskMSnExp_other_methods.R
MSnbase/tests/testthat/test_ProcessingStep.R
MSnbase/tests/testthat/test_ReportersIons.R
MSnbase/tests/testthat/test_Spectrum.R
MSnbase/tests/testthat/test_Spectrum_Constructor.R
MSnbase/tests/testthat/test_average.R
MSnbase/tests/testthat/test_cache.R
MSnbase/tests/testthat/test_centroided.R
MSnbase/tests/testthat/test_compfnames.R
MSnbase/tests/testthat/test_defunct.R
MSnbase/tests/testthat/test_equalMSnExps.R
MSnbase/tests/testthat/test_fileNames.R
MSnbase/tests/testthat/test_filterNA.R
MSnbase/tests/testthat/test_foi.R
MSnbase/tests/testthat/test_fragments.R
MSnbase/tests/testthat/test_iPQF.R
MSnbase/tests/testthat/test_impute.R
MSnbase/tests/testthat/test_io.R
MSnbase/tests/testthat/test_matching.R
MSnbase/tests/testthat/test_mzR-funs.R
MSnbase/tests/testthat/test_nadata.R
MSnbase/tests/testthat/test_plotting.R
MSnbase/tests/testthat/test_purity.R
MSnbase/tests/testthat/test_quant.R
MSnbase/tests/testthat/test_readMSData2.R
MSnbase/tests/testthat/test_readWriteMgfData.R
MSnbase/tests/testthat/test_topN.R
MSnbase/tests/testthat/test_trimws.R
MSnbase/tests/testthat/test_updateObjects.R
MSnbase/tests/testthat/test_utils.R
MSnbase/vignettes
MSnbase/vignettes/Bugs.tex
MSnbase/vignettes/Foreword.tex
MSnbase/vignettes/MSnbase-demo.Rnw
MSnbase/vignettes/MSnbase-development.Rnw
MSnbase/vignettes/MSnbase-io.Rnw
MSnbase/vignettes/MSnbase.bib
MSnbase/vignettes/NOTES.org
MSnbase/vignettes/NoteAboutSpeedAndMemory.tex
MSnbase/vignettes/benchmarking.Rmd
MSnbase/vignettes/itraqchem.pdf
MSnbase/vignettes/msnset.png
MSnbase/vignettes/plot2d-figure.png
MSnbase/vignettes/plotDensity-figure.png
MSnbase/vignettes/plotMzDelta-pride12011.pdf
MSnbase/vignettes/tmt10comp.pdf