Files in Bioconductor-mirror/MSnbase
Base Functions and Classes for Mass Spectrometry and Proteomics

.Rbuildignore
.Rinstignore
.gitignores/all
.gitignores/devel
.travis.yml
CONDUCT.md
DESCRIPTION
NAMESPACE
NEWS
NEWS.md R/AllClassUnions.R R/AllGenerics.R R/DataClasses.R R/MzTab.R R/NTR.R R/RcppExports.R R/TMT10.R R/TMT6.R R/TMT7.R R/averageMSnSet.R R/cache.R R/combineFeatures.R R/compfnames.R R/environment.R R/foi.R R/functions-Chromatogram.R R/functions-Chromatograms.R R/functions-MIAPE.R R/functions-MSnExp.R R/functions-MSnProcess.R R/functions-MSnSet.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-fragments.R R/functions-mzR.R R/header.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-Chromatograms.R R/methods-MIAPE.R R/methods-MSnExp.R R/methods-MSnProcess.R R/methods-MSnSet.R R/methods-MSnSetList.R R/methods-NAnnotatedDataFrame.R R/methods-OnDiskMSnExp.R R/methods-ProcessingStep.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/missing-data.R R/nadata.R R/nav.R R/options.R R/plotting-MSnExp.R R/plotting-MSnSet.R R/plotting-OnDiskMSnExp.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/readMSData.R R/readMSData2.R R/readMSnSet.R R/readMzXMLData.R R/readWriteMgfData.R R/readWriteMzTab.R R/utils.R R/zzz.R README.Rmd README.md
data/TMT10.RData
data/TMT10ETD.RData
data/TMT10HCD.RData
data/TMT6.RData
data/TMT6b.RData
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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
docs/articles/Bugs.md
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docs/articles/Figures/MSnbase-io-in.tex
docs/articles/Figures/MSnbase-io-out.png
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docs/articles/MSnbase-demo_files/figure-html/spectrumPlot-1.png
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docs/articles/MSnbase-io.html
docs/articles/MSnbase.bib
docs/articles/benchmarking.html
docs/articles/benchmarking_cache/html/__packages
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docs/index.html
docs/jquery.sticky-kit.min.js
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docs/pkgdown.css
docs/pkgdown.js
docs/reference/Chromatogram-class.html
docs/reference/Chromatograms-class.html
docs/reference/FeatComp-class.html
docs/reference/FeaturesOfInterest-class.html
docs/reference/MIAPE-class.html
docs/reference/MSmap-class.html
docs/reference/MSnExp-class.html
docs/reference/MSnProcess-class.html
docs/reference/MSnSet-class.html
docs/reference/MSnSetList-class.html
docs/reference/MSnbase-package.html
docs/reference/MSnbaseOptions.html
docs/reference/MzTab-class.html
docs/reference/NAnnotatedDataFrame-class.html
docs/reference/OnDiskMSnExp-class.html
docs/reference/ProcessingStep-class.html
docs/reference/ReporterIons-class.html
docs/reference/Spectrum-class.html
docs/reference/Spectrum1-class.html
docs/reference/Spectrum2-class.html
docs/reference/TMT6.html
docs/reference/addIdentificationData-methods.html
docs/reference/aggvar.html
docs/reference/averageMSnSet.html
docs/reference/bin-methods.html
docs/reference/calculateFragments-methods.html
docs/reference/chromatogram-MSnExp-method-14.png
docs/reference/chromatogram-MSnExp-method-6.png
docs/reference/chromatogram-MSnExp-method.html
docs/reference/clean-methods.html
docs/reference/combineFeatures.html
docs/reference/commonFeatureNames.html
docs/reference/compareMSnSets.html
docs/reference/compareSpectra-methods.html
docs/reference/defunct.html
docs/reference/estimateNoise-method.html
docs/reference/exprsToRatios-methods.html
docs/reference/extractPrecSpectra-methods.html
docs/reference/factorsAsStrings.html
docs/reference/featureCV.html
docs/reference/fillUp.html
docs/reference/filterIdentificationDataFrame.html
docs/reference/formatRt.html
docs/reference/get.amino.acids.html
docs/reference/get.atomic.mass.html
docs/reference/getVariableName.html
docs/reference/grepEcols.html
docs/reference/iPQF.html
docs/reference/iTRAQ4.html
docs/reference/imageNA2.html
docs/reference/impute-methods.html
docs/reference/index.html
docs/reference/itraqdata.html
docs/reference/itraqdata.mgf
docs/reference/listOf.html
docs/reference/makeCamelCase.html
docs/reference/makeNaData.html
docs/reference/missing-data.html
docs/reference/mzRident2dfr.html
docs/reference/nFeatures.html
docs/reference/nQuants.html
docs/reference/naplot-2.png
docs/reference/naplot.html
docs/reference/navMS.html
docs/reference/normToReference.html
docs/reference/normalise-methods.html
docs/reference/npcv.html
docs/reference/pSet-class.html
docs/reference/pickPeaks-method.html
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docs/reference/plotSpectrumSpectrum-methods-4.png
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docs/reference/precSelection.html
docs/reference/purityCorrect-methods.html
docs/reference/quantify-methods.html
docs/reference/readMSData.html
docs/reference/readMSnSet.html
docs/reference/readMgfData.html
docs/reference/readMzIdData.html
docs/reference/readMzTabData.html
docs/reference/readMzTabData_v0.9.html
docs/reference/reduce-data.frame-method.html
docs/reference/removeNoId-methods.html
docs/reference/removePeaks-methods.html
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docs/reference/selectFeatureData.html
docs/reference/smooth-methods.html
docs/reference/trimMz-methods.html
docs/reference/updateObject-methods.html
docs/reference/writeMgfData-methods.html
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/Chromatograms-class.Rd man/FeatComp-class.Rd man/FeaturesOfInterest-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/MSnbase-package.Rd man/MSnbaseOptions.Rd man/MzTab-class.Rd man/NAnnotatedDataFrame-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/commonFeatureNames.Rd man/compareMSnSets.Rd man/compareSpectra-methods.Rd man/defunct.Rd man/estimateNoise-method.Rd man/exprsToRatios-methods.Rd man/extractPrecSpectra-methods.Rd man/factorsAsStrings.Rd man/featureCV.Rd man/fillUp.Rd man/filterIdentificationDataFrame.Rd man/formatRt.Rd man/get.amino.acids.Rd man/get.atomic.mass.Rd man/getVariableName.Rd man/grepEcols.Rd man/iPQF.Rd man/iTRAQ4.Rd man/imageNA2.Rd man/impute-methods.Rd man/itraqdata.Rd man/listOf.Rd man/makeCamelCase.Rd man/makeNaData.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/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/writeMgfData-methods.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_MzTab.R tests/testthat/test_MzTab_09.R tests/testthat/test_NAnnotatedDataFrame.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_ProcessingStep.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_compfnames.R tests/testthat/test_defunct.R tests/testthat/test_equalMSnExps.R tests/testthat/test_fileNames.R tests/testthat/test_filterEmptySpectra.R tests/testthat/test_filterNA.R tests/testthat/test_foi.R tests/testthat/test_fragments.R tests/testthat/test_functions-Chromatogram.R tests/testthat/test_functions-Chromatograms.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-Chromatograms.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_readMSData2.R tests/testthat/test_readWriteMgfData.R tests/testthat/test_topN.R tests/testthat/test_trimws.R tests/testthat/test_updateObjects.R tests/testthat/test_utils.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-demo.Rmd vignettes/MSnbase-development.Rmd vignettes/MSnbase-io.Rmd
vignettes/MSnbase.bib
vignettes/benchmarking.Rmd
Bioconductor-mirror/MSnbase documentation built on Aug. 12, 2017, 5:08 p.m.