Files in lgatto/MSnbase

Base Functions and Classes for Mass Spectrometry and Proteomics

.Rbuildignore

.Rinstignore

.editorconfig

.github/.gitignore

.github/workflows/check-bioc.yml

.gitignore

CONDUCT.md

DESCRIPTION

NAMESPACE

NEWS.md R/AllClassUnions.R R/AllGenerics.R R/DataClasses.R R/MzTab.R R/NAnnotatedDataFrame.R R/NTR.R R/RcppExports.R R/TMT10.R R/TMT11.R R/TMT16.R R/TMT6.R R/TMT7.R R/averageMSnSet.R R/cache.R R/coerce.R R/combineFeatures.R R/compfnames.R R/environment.R R/fData-utils.R R/fdata-selection.R R/foi.R R/functions-Chromatogram.R R/functions-MChromatograms.R R/functions-MIAPE.R R/functions-MSnExp.R R/functions-MSnProcess.R R/functions-MSnSet.R R/functions-MSpectra.R R/functions-OnDiskMSnExp.R R/functions-ReporterIons.R R/functions-Spectrum.R R/functions-Spectrum1.R R/functions-Spectrum2.R R/functions-addIdentificationData.R R/functions-mzR.R R/functions-plotting.R R/hmap.R R/iPQF.R R/iTRAQ4.R R/iTRAQ5.R R/iTRAQ8.R R/iTRAQ9.R R/imputation.R R/map.R R/matching.R R/methods-Chromatogram.R R/methods-MChromatograms.R R/methods-MIAPE.R R/methods-MSnExp.R R/methods-MSnProcess.R R/methods-MSnSet.R R/methods-MSnSetList.R R/methods-MSpectra.R R/methods-OnDiskMSnExp.R R/methods-ReporterIons.R R/methods-Spectrum.R R/methods-Spectrum1.R R/methods-Spectrum2.R R/methods-all.equal.R R/methods-filters.R R/methods-fragments.R R/methods-mzR.R R/methods-other.R R/methods-pSet.R R/methods-updateObjectTo.R R/methods-write.R R/missing-data.R R/nadata.R R/nav.R R/options.R R/plotting-MSnExp.R R/plotting-MSnSet.R R/plotting-Spectrum.R R/plotting-Spectrum1.R R/plotting-Spectrum2.R R/plotting-dataframe.R R/quantitation-MS2-isobaric.R R/quantitation-MS2-labelfree.R R/readChromData.R R/readMSData.R R/readMSData2.R R/readMSnSet.R R/readMzXMLData.R R/readWriteMgfData.R R/readWriteMzTab.R R/utils.R R/writeMSData.R R/zzz.R README.md

data/TMT10.RData

data/TMT10ETD.RData

data/TMT10HCD.RData

data/TMT11.RData

data/TMT11HCD.RData

data/TMT16.RData

data/TMT16HCD.RData

data/TMT6.RData

data/TMT6b.RData

data/TMT7.RData

data/TMT7b.RData

data/iTRAQ4.RData

data/iTRAQ5.RData

data/iTRAQ8.RData

data/iTRAQ9.RData

data/itraqdata.RData

data/msnset.rda

data/msnset2.rda

data/naset.rda

inst/CITATION

inst/extdata/M.rda

inst/extdata/M2.rda

inst/extdata/TMT6plexPurityCorrections.csv

inst/extdata/dummyiTRAQ.mzXML

inst/extdata/dummyiTRAQ.mzid

inst/extdata/iTRAQ4plexPurityCorrections.csv

inst/extdata/iTRAQ8plexPurityCorrections.csv

inst/extdata/ipqfres.rda

inst/extdata/msx.rda

inst/extdata/msx0.rda

inst/extdata/test.mgf

inst/scripts/benchmarking.R inst/scripts/make_msx.R inst/scripts/naset.R inst/scripts/torture.R man/Chromatogram-class.Rd man/FeatComp-class.Rd man/FeaturesOfInterest-class.Rd man/MChromatograms-class.Rd man/MIAPE-class.Rd man/MSmap-class.Rd man/MSnExp-class.Rd man/MSnProcess-class.Rd man/MSnSet-class.Rd man/MSnSetList-class.Rd man/MSnbaseOptions.Rd man/MSpectra.Rd man/MzTab-class.Rd man/OnDiskMSnExp-class.Rd man/ProcessingStep-class.Rd man/ReporterIons-class.Rd man/Spectrum-class.Rd man/Spectrum1-class.Rd man/Spectrum2-class.Rd man/TMT6.Rd man/addIdentificationData-methods.Rd man/aggvar.Rd man/averageMSnSet.Rd man/bin-methods.Rd man/calculateFragments-methods.Rd man/chromatogram-MSnExp-method.Rd man/clean-methods.Rd man/combineFeatures.Rd man/combineSpectra.Rd man/combineSpectraMovingWindow.Rd man/commonFeatureNames.Rd man/compareMSnSets.Rd man/compareSpectra-methods.Rd man/consensusSpectrum.Rd man/defunct.Rd man/estimateMzResolution.Rd man/estimateMzScattering.Rd man/estimateNoise-method.Rd man/extractPrecSpectra-methods.Rd man/extractSpectraData.Rd man/fData-utils.Rd man/factorsAsStrings.Rd man/featureCV.Rd man/fillUp.Rd man/filterIdentificationDataFrame.Rd man/formatRt.Rd man/getVariableName.Rd man/grepEcols.Rd man/hasSpectraOrChromatograms.Rd man/iPQF.Rd man/iTRAQ4.Rd man/imageNA2.Rd man/impute.Rd man/isCentroidedFromFile.Rd man/itraqdata.Rd man/listOf.Rd man/makeCamelCase.Rd man/makeNaData.Rd man/meanMzInts.Rd man/missing-data.Rd man/mzRident2dfr.Rd man/nFeatures.Rd man/nQuants.Rd man/naplot.Rd man/navMS.Rd man/normToReference.Rd man/normalise-methods.Rd man/npcv.Rd man/pSet-class.Rd man/pickPeaks-method.Rd man/plot-methods.Rd man/plot2d-methods.Rd man/plotDensity-methods.Rd man/plotMzDelta-methods.Rd man/plotNA-methods.Rd man/plotSpectrumSpectrum-methods.Rd man/precSelection.Rd man/purityCorrect-methods.Rd man/quantify-methods.Rd man/readMSData.Rd man/readMSnSet.Rd man/readMgfData.Rd man/readMzIdData.Rd man/readMzTabData.Rd man/readMzTabData_v0.9.Rd man/readSRMData.Rd man/reduce-data.frame-method.Rd man/removeNoId-methods.Rd man/removePeaks-methods.Rd man/removeReporters-methods.Rd man/selectFeatureData.Rd man/smooth-methods.Rd man/trimMz-methods.Rd man/updateObject-methods.Rd man/writeMSData.Rd man/writeMgfData-methods.Rd man/writeMzTabData.Rd

src/MSnbase.h

src/RcppExports.cpp

src/Spectrum1_class.c

src/Spectrum2_class.c

src/imp_neighbour_avg.cpp

src/utils.c

tests/testthat.R tests/testthat/dont_test_plotMzDelata.R tests/testthat/test_MIAPE.R tests/testthat/test_MSmap.R tests/testthat/test_MSnExp.R tests/testthat/test_MSnExpFilters.R tests/testthat/test_MSnExpSubsetting.R tests/testthat/test_MSnProcess.R tests/testthat/test_MSnSet.R tests/testthat/test_MSnSetList.R tests/testthat/test_MzTab.R tests/testthat/test_MzTab_09.R tests/testthat/test_NTR.R tests/testthat/test_OnDiskMSnExp.R tests/testthat/test_OnDiskMSnExp2.R tests/testthat/test_OnDiskMSnExp_other_methods.R tests/testthat/test_ReportersIons.R tests/testthat/test_Spectrum.R tests/testthat/test_Spectrum_Constructor.R tests/testthat/test_average.R tests/testthat/test_cache.R tests/testthat/test_centroided.R tests/testthat/test_coerce.R tests/testthat/test_compfnames.R tests/testthat/test_defunct.R tests/testthat/test_equalMSnExps.R tests/testthat/test_fdata-selection.R tests/testthat/test_fileNames.R tests/testthat/test_filterEmptySpectra.R tests/testthat/test_filterNA.R tests/testthat/test_foi.R tests/testthat/test_functions-Chromatogram.R tests/testthat/test_functions-MChromatograms.R tests/testthat/test_functions-MSpectra.R tests/testthat/test_functions-plotting.R tests/testthat/test_iPQF.R tests/testthat/test_id.R tests/testthat/test_impute.R tests/testthat/test_io.R tests/testthat/test_matching.R tests/testthat/test_methods-Chromatogram.R tests/testthat/test_methods-MChromatograms.R tests/testthat/test_methods-MSpectra.R tests/testthat/test_missing-data.R tests/testthat/test_mzR-funs.R tests/testthat/test_nadata.R tests/testthat/test_nav.R tests/testthat/test_options.R tests/testthat/test_plotting.R tests/testthat/test_purity.R tests/testthat/test_quant.R tests/testthat/test_readChromData.R tests/testthat/test_readMSData.R tests/testthat/test_readMSData2.R tests/testthat/test_readWriteMgfData.R tests/testthat/test_robust.R tests/testthat/test_topN.R tests/testthat/test_trimws.R tests/testthat/test_updateObjects.R tests/testthat/test_utils.R tests/testthat/test_writeMSData.R vignettes/Bugs.md

vignettes/Figures/MSnbase-io-in.png

vignettes/Figures/MSnbase-io-in.tex

vignettes/Figures/MSnbase-io-out.png

vignettes/Figures/MSnbase-io-out.tex

vignettes/Figures/Makefile

vignettes/Figures/itraqchem.pdf

vignettes/Figures/itraqchem.png

vignettes/Figures/msnset.png

vignettes/Figures/plot2d-figure.png

vignettes/Figures/plotDensity-figure.png

vignettes/Figures/plotMzDelta-pride12011.pdf

vignettes/Figures/plotMzDelta-pride12011.png

vignettes/Figures/tmt10comp.pdf

vignettes/Figures/tmt10comp.png

vignettes/Foreword.md

vignettes/MSnbase.bib

vignettes/v01-MSnbase-demo.Rmd vignettes/v02-MSnbase-io.Rmd vignettes/v03-MSnbase-centroiding.Rmd vignettes/v04-benchmarking.Rmd vignettes/v05-MSnbase-development.Rmd

lgatto/MSnbase documentation built on March 14, 2024, 7:06 a.m.