MSnbase: Base Functions and Classes for MS-based Proteomics

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

AuthorLaurent 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 publicationNone
MaintainerLaurent Gatto <lg390@cam.ac.uk>
LicenseArtistic-2.0
Version2.0.2
https://github.com/lgatto/MSnbase

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.