MSnbase
Base Functions and Classes for Mass Spectrometry and Proteomics

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Source code
162
Man pages
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MSnbase: Base Functions and Classes for Mass Spectrometry and Proteomics
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API

API for MSnbase
Base Functions and Classes for Mass Spectrometry and Proteomics

Global functions
$,MChromatograms-method Man page
$,pSet-method Man page
$<-,MChromatograms-method Man page
$<-,pSet-method Man page
.addCharacterIdentificationData Source code
.addDataFrameIdentificationData Source code
.addMzIDIdentificationData Source code
.addMzRidentIdentificationData Source code
.applyFun2IndividualSpectraOfFile Source code
.applyFun2SpectraOfFileMulti Source code
.bin_Chromatogram Source code
.bin_MChromatograms Source code
.bin_values Source code
.calcCompNumbers Source code
.calculateFragments Source code
.combineFeatures Source code
.combineMovingWindow Source code
.combine_data.frame Source code
.compStrings Source code
.density Source code
.estimate_mz_resolution Source code
.estimate_mz_scattering Source code
.estimate_mz_scattering_list Source code
.extractMultipleChromatograms Source code
.fileExt Source code
.filterNA Source code
.filterSpectraHierarchy Source code
.findPeakValley Source code
.firstMsLevel Source code
.fix_breaks Source code
.get.amino.acids Source code
.get.atomic.mass Source code
.group_mz_values Source code
.guessSoftwareProcessing Source code
.header Source code
.isCentroided Source code
.isCentroidedFromFile Source code
.make_naked_matrix_from_MSpectra Source code
.mz_chromatograms Source code
.neutralLoss Source code
.onAttach Source code
.onLoad Source code
.on_disk_split_by_file Source code
.openMSfile Source code
.pattern_to_cv Source code
.plotChromatogram Source code
.plotChromatogramList Source code
.plotSingleSpectrum Source code
.plotSpectrumVsSpectrum Source code
.plotXIC Source code
.polarity_char Source code
.preparePlotNAData Source code
.reduce_list Source code
.referenceFraction Source code
.referenceFractionValues Source code
.rowMaxs Source code
.sameNbCol Source code
.sameNbRow Source code
.selectShinyFeatureData Source code
.selectTextFeatureData Source code
.short_spectrum_info Source code
.show_MSpectra Source code
.slotNames0 Source code
.spectrum_header Source code
.summariseRows Source code
.terminalModifications Source code
.testReadMSDataInput Source code
.topIdx Source code
.validChromatogram Source code
.validMChromatograms Source code
.versionToNum Source code
.vertical_sub_layout Source code
.writeMSData Source code
.writeSingleMSData Source code
Chromatogram Man page Source code
Chromatogram-class Man page
FeatComp-class Man page
FeaturesOfInterest Man page
FeaturesOfInterest,character,character,MSnSet-method Man page
FeaturesOfInterest,character,character,missing-method Man page
FeaturesOfInterest-class Man page
FeaturesOfInterest-methods Man page
FoICollection Man page
FoICollection,list-method Man page
FoICollection,missing-method Man page
FoICollection-class Man page
FoICollection-methods Man page
MAplot,MSnSet-method Man page
MChromatograms Man page Source code
MChromatograms-class Man page
MIAPE Man page
MIAPE-class Man page
MSmap Man page
MSmap,OnDiskMSnExp-method Man page
MSmap,mzRpwiz-method Man page
MSmap,mzRramp-method Man page
MSmap,mzRraw-method Man page
MSmap-class Man page
MSmap-method Man page
MSnExp Man page
MSnExp-class Man page
MSnExp.size Source code
MSnProcess Man page
MSnProcess-class Man page
MSnSet Man page Source code
MSnSet-class Man page
MSnSetList Man page Source code
MSnSetList-class Man page
MSnbase-defunct Man page
MSnbase-deprecated Man page
MSnbaseOptions Man page Source code
MSpectra Man page Source code
MSpectra-class Man page
MzTab Man page Source code
MzTab-class Man page
NAnnotatedDataFrame Man page
NAnnotatedDataFrame-class Man page
NTR Man page
OnDiskMSnExp Man page
OnDiskMSnExp-class Man page
ProcessingStep Man page Source code
ProcessingStep-class Man page
ProcessingStep:OnDiskMSnExp Man page
ReporterIons Man page
ReporterIons-class Man page
SAF Source code
SI Source code
Spectra1_mz_sorted Source code
Spectra2_mz_sorted Source code
Spectrum Man page
Spectrum-class Man page
Spectrum1 Man page Source code
Spectrum1-class Man page
Spectrum1_mz_sorted Source code
Spectrum2 Man page Source code
Spectrum2-class Man page
Spectrum2_mz_sorted Source code
TMT10 Man page
TMT10ETD Man page
TMT10HCD Man page
TMT11 Man page
TMT11HCD Man page
TMT6 Man page
TMT6b Man page
TMT7 Man page
TMT7b Man page
[,FoICollection,ANY,ANY,ANY-method Man page
[,FoICollection,ANY,ANY-method Man page
[,FoICollection-method Man page
[,MChromatograms,ANY,ANY,ANY-method Man page
[,MSnSet,ANY,ANY,ANY-method Man page
[,MSnSet,ANY,ANY-method Man page
[,MSnSet-method Man page
[,MSnSetList,ANY,ANY,ANY-method Man page
[,MSnSetList,ANY,missing,missing-method Man page
[,OnDiskMSnExp,ANY,ANY,ANY-method Man page
[,OnDiskMSnExp,logicalOrNumeric,missing,missing-method Man page
[,ReporterIons,ANY,ANY,ANY-method Man page
[,ReporterIons,ANY,ANY-method Man page
[,ReporterIons-method Man page
[,pSet,ANY,ANY,ANY-method Man page
[,pSet,ANY,ANY-method Man page
[,pSet-method Man page
[<-,MChromatograms-method Man page
[[,FoICollection,ANY,ANY-method Man page
[[,FoICollection-method Man page
[[,MSnSetList,ANY,ANY-method Man page
[[,MSnSetList,ANY,missing-method Man page
[[,OnDiskMSnExp,ANY,ANY,missing-method Man page
[[,OnDiskMSnExp,ANY,ANY-method Man page
[[,OnDiskMSnExp,ANY,missing,missing-method Man page
[[,OnDiskMSnExp-method Man page
[[,pSet,ANY,ANY-method Man page
[[,pSet-method Man page
abstract,MIAPE-method Man page
abstract,pSet-method Man page
acquisitionNum Man page
acquisitionNum,MSnSet-method Man page
acquisitionNum,MSpectra-method Man page
acquisitionNum,OnDiskMSnExp-method Man page
acquisitionNum,Spectrum-method Man page
acquisitionNum,pSet-method Man page
addFeaturesOfInterest Man page
addFeaturesOfInterest,FeaturesOfInterest,FoICollection-method Man page
addFeaturesOfInterest-methods Man page
addIdentificationData Man page
addIdentificationData,MSnExp,character-method Man page
addIdentificationData,MSnExp,data.frame-method Man page
addIdentificationData,MSnExp,mzID-method Man page
addIdentificationData,MSnExp,mzIDClasses-method Man page
addIdentificationData,MSnExp,mzIDCollection-method Man page
addIdentificationData,MSnExp,mzRident-method Man page
addIdentificationData,MSnSet,character-method Man page
addIdentificationData,MSnSet,data.frame-method Man page
addIdentificationData,MSnSet,mzID-method Man page
addIdentificationData,MSnSet,mzIDClasses-method Man page
addIdentificationData,MSnSet,mzIDCollection-method Man page
addIdentificationData,MSnSet,mzRident-method Man page
addIdentificationData-methods Man page
addMSnSetMetadata Man page Source code
addMzTabMetadata Source code
aggregationFun Man page Source code
aggvar Man page Source code
all.equal,MSnExp,MSnExp-method Man page
all.equal,MSnExp,OnDiskMSnExp-method Man page
all.equal,OnDiskMSnExp,MSnExp-method Man page
all.equal,OnDiskMSnExp,OnDiskMSnExp-method Man page
analyser Man page
analyser,MIAPE-method Man page
analyser,MSnSet-method Man page
analyser,pSet-method Man page
analyserDetails Man page
analyserDetails,MIAPE-method Man page
analyserDetails,pSet-method Man page
analyzer Man page
analyzer,MIAPE-method Man page
analyzer,MSnSet-method Man page
analyzer,pSet-method Man page
analyzerDetails Man page
analyzerDetails,MIAPE-method Man page
analyzerDetails,pSet-method Man page
as Man page
as.ExpressionSet.MSnSet Man page Source code
as.IBSpectra.MSnSet Source code
as.MIAME.MIAPE Man page Source code
as.MSnExp.OnDiskMSnExp Man page Source code
as.MSnSet.ExpressionSet Man page Source code
as.data.frame,Chromatogram-method Man page
as.data.frame.MSmap Source code
as.data.frame.MSnExp Man page Source code
as.data.frame.MSnSet Man page Source code
as.data.frame.Spectrum Man page Source code
as.data.frame.mzRident Man page Source code
as.matrix.FoICollection Man page Source code
assayData,OnDiskMSnExp-method Man page
assayData,pSet-method Man page
averageMSnSet Man page Source code
bin Man page
bin,Chromatogram-method Man page
bin,MChromatograms-method Man page
bin,MSnExp-method Man page Man page
bin,OnDiskMSnExp-method Man page
bin,Spectrum-method Man page Man page
bin-methods Man page
bin_MSnExp Source code
bin_Spectra Source code
bin_Spectrum Source code
bpi Man page
bpi,OnDiskMSnExp-method Man page
cacheEnvIsLocked Source code
calculateFragments Man page
calculateFragments,character,Spectrum2-method Man page
calculateFragments,character,missing-method Man page
calculateFragments_Spectrum2 Source code
centroided Man page
centroided,MSpectra-method Man page
centroided,OnDiskMSnExp-method Man page
centroided,Spectrum-method Man page
centroided,pSet-method Man page
centroided<- Man page
centroided<-,OnDiskMSnExp,logical-method Man page
centroided<-,Spectrum,ANY-method Man page
centroided<-,Spectrum,logical-method Man page
centroided<-,pSet,ANY-method Man page
centroided<-,pSet,logical-method Man page
checkHeader Source code
chromatogram Man page
chromatogram,MSnExp-method Man page
class:MIAPE Man page
class:MSnExp Man page
class:MSnProcess Man page
class:MSnSet Man page
class:MzTab Man page
class:NAnnotatedDataFrame Man page
class:OnDiskMSnExp Man page
class:ReporterIons Man page
class:Spectrum Man page
class:Spectrum1 Man page
class:Spectrum2 Man page
class:pSet Man page
clean Man page
clean,Chromatogram-method Man page
clean,MChromatograms-method Man page
clean,MSnExp-method Man page Man page
clean,MSpectra-method Man page
clean,OnDiskMSnExp-method Man page
clean,Spectrum-method Man page Man page
clean-methods Man page
clean_MSnExp Source code
clean_Spectrum Source code
coerce,AnnotatedDataFrame,list-method Man page
coerce,ExpressionSet,MSnSet-method Man page
coerce,FoICollection,matrix-method Man page
coerce,IBSpectra,MSnSet-method Man page
coerce,MIAPE,MIAME-method Man page
coerce,MIAxE,list-method Man page
coerce,MSmap,data.frame-method Man page
coerce,MSnExp,MSpectra-method Man page
coerce,MSnExp,data.frame-method Man page
coerce,MSnProcess,list-method Man page
coerce,MSnSet,ExpressionSet-method Man page
coerce,MSnSet,SummarizedExperiment-method Man page
coerce,MSnSet,data.frame-method Man page
coerce,MSpectra,MSnExp-method Man page
coerce,MSpectra,list-method Man page
coerce,MzTab,MSnSetList-method Man page
coerce,OnDiskMSnExp,MSnExp-method Man page
coerce,Spectrum,data.frame-method Man page
coerce,SummarizedExperiment,MSnSet-method Man page
coerce,matrix,MChromatograms-method Man page
coerce,mzRident,data.frame-method Man page
collisionEnergy Man page
collisionEnergy,MSpectra-method Man page
collisionEnergy,OnDiskMSnExp-method Man page
collisionEnergy,Spectrum-method Man page
collisionEnergy,pSet-method Man page
colnames<-,MChromatograms-method Man page
combine,MIAPE,MIAPE-method Man page
combine,MSnProcess,MSnProcess-method Man page
combine,MSnSet,MSnSet-method Man page
combineFeatures Man page
combineFeatures,MSnSet-method Man page
combineFeaturesL Source code
combineFeaturesV Source code
combineMatrixFeatures Source code
combineSpectra Man page
combineSpectra,MSnExp-method Man page
combineSpectra,MSpectra-method Man page
combineSpectraMovingWindow Man page Source code
comments Man page Source code
common Man page
common,FeatComp-method Man page
common,methods Man page
commonFeatureNames Man page Source code
commonPeaks Source code
compareMSnSets Man page Source code
compareSpectra Man page
compareSpectra,MSnExp,missing-method Man page
compareSpectra,MSnExp-method Man page
compareSpectra,OnDiskMSnExp,missing-method Man page
compareSpectra,Spectrum,Spectrum-method Man page
compareSpectra,Spectrum-method Man page
compareSpectra-methods Man page
compare_MSnExp Source code
compare_Spectra Source code
compfnames Man page
compfnames,MSnSet,MSnSet-method Man page
compfnames,list,missing-method Man page
compfnames-methods Man page
consensusSpectrum Man page Source code
countAndPrint Source code
count_MSnSet Source code
cramer4 Source code
curveData Source code
curveStats_Spectrum Source code
defaultNeutralLoss Man page Source code
descendPeak Source code
description,FeaturesOfInterest-method Man page
description,FoICollection-method Man page
description,MSnSet-method Man page
description,ReporterIons-method Man page
description,pSet-method Man page
detectorType Man page
detectorType,MIAPE-method Man page
detectorType,MSnSet-method Man page
detectorType,pSet-method Man page
dim Man page
dim,MSmap-method Man page
dim,MSnSet-method Man page
dim,NAnnotatedDataFrame-method Man page
dim,pSet-method Man page
dotproduct Source code
droplevels.MSnSet Man page Source code
equalMSnExps Source code
estimateMzResolution Man page
estimateMzResolution,MSnExp-method Man page
estimateMzResolution,Spectrum-method Man page
estimateMzScattering Man page Source code
estimateNoise Man page
estimateNoise,MSnExp-method Man page
estimateNoise,OnDiskMSnExp-method Man page
estimateNoise,Spectrum-method Man page
estimateNoise-methods Man page
estimateNoise_Spectrum Source code
executeProcessingStep Man page Source code
expandFeatureVars Man page Source code
expemail Man page
expemail,MIAPE-method Man page
expemail,MSnSet-method Man page
expemail,pSet-method Man page
experimentData,pSet-method Man page
experimentData<-,MSnSet,MIAPE-method Man page
expinfo,MIAPE-method Man page
exprs,MSnSet-method Man page
exptitle Man page
exptitle,MIAPE-method Man page
exptitle,MSnSet-method Man page
exptitle,pSet-method Man page
extractMgfSpectrum2Info Source code
extractPrecSpectra Man page
extractPrecSpectra,MSnExp,numeric-method Man page
extractPrecSpectra,MSnExp-method Man page
extractPrecSpectra,OnDiskMSnExp,numeric-method Man page
extractPrecSpectra-methods Man page
extractPrecSpectra_MSnExp Source code
extractSpectra Man page
extractSpectra,MSnExp,logical-method Man page
extractSpectra,MSnExp-method Man page
extractSpectraData Man page Source code
fData,MChromatograms-method Man page
fData,MSnSetList-method Man page
fData,pSet-method Man page
fData<-,MChromatograms,ANY-method Man page
fData<-,MSnSet,data.frame-method Man page
fData<-,MSnSetList,DataFrame-method Man page
fData<-,pSet,data.frame-method Man page
factorsAsStrings Man page Source code
fastquant_max Source code
featureCV Man page Source code
featureData,MChromatograms-method Man page
featureData,pSet-method Man page
featureData<-,MChromatograms,ANY-method Man page
featureNames,MChromatograms-method Man page
featureNames,OnDiskMSnExp-method Man page
featureNames,pSet-method Man page
featureNames<-,MChromatograms-method Man page
featureNames<-,OnDiskMSnExp,ANY-method Man page
featureNames<-,OnDiskMSnExp-method Man page
fileName,MSmap-method Man page
fileName,MzTab-method Man page
fileNames Man page
fileNames,MSmap-method Man page
fileNames,MSnProcess-method Man page
fileNames,MSnSet-method Man page
fileNames,MzTab-method Man page
fileNames,pSet-method Man page
fillUp Man page Source code
filterAcquisitionNum Man page
filterAcquisitionNum,MSnExp-method Man page
filterAcquisitionNum,OnDiskMSnExp-method Man page
filterEmptySpectra Man page
filterEmptySpectra,MSnExp-method Man page
filterEmptySpectra,OnDiskMSnExp-method Man page
filterFile Man page
filterFile,MSnExp-method Man page
filterFile,OnDiskMSnExp-method Man page
filterIdentificationDataFrame Man page Source code
filterIsolationWindow Man page
filterIsolationWindow,MSnExp-method Man page
filterMsLevel Man page
filterMsLevel,MSnExp-method Man page
filterMsLevel,MSnSet-method Man page
filterMsLevel,MSpectra-method Man page
filterMsLevel,OnDiskMSnExp-method Man page
filterMz Man page
filterMz,MSnExp-method Man page
filterMz,MSpectra-method Man page
filterMz,OnDiskMSnExp-method Man page
filterMz,Spectrum-method Man page
filterMz-methods Man page
filterNA Man page
filterNA,MSnSet-method Man page
filterNA,matrix-method Man page
filterPolarity Man page
filterPolarity,MSnExp-method Man page
filterPolarity,OnDiskMSnExp-method Man page
filterPrecursorMz Man page
filterPrecursorMz,MSnExp-method Man page
filterPrecursorScan Man page
filterPrecursorScan,MSnExp-method Man page
filterPrecursorScan,OnDiskMSnExp-method Man page
filterRt Man page
filterRt,Chromatogram-method Man page
filterRt,MSnExp-method Man page
filterRt,OnDiskMSnExp-method Man page
filterZero Man page
filterZero,MSnSet-method Man page
filterZero,matrix-method Man page
filtermz,Spectrum,numeric-method Man page
fnamesIn Man page
fnamesIn,FeaturesOfInterest,MSnSet-method Man page
fnamesIn,FeaturesOfInterest,data.frame-method Man page
fnamesIn,FeaturesOfInterest,matrix-method Man page
fnamesIn-methods Man page
foi Man page
foi,FeaturesOfInterest-method Man page
foi,FoICollection-method Man page
foi-methods Man page
formatFileSpectrumNames Source code
formatRt Man page Source code
fromFile Man page
fromFile,Chromatogram-method Man page
fromFile,MSnSet-method Man page
fromFile,MSpectra-method Man page
fromFile,OnDiskMSnExp-method Man page
fromFile,Spectrum-method Man page
fromFile,pSet-method Man page
fvarLabels,MChromatograms-method Man page
fvarLabels,pSet-method Man page
fvarMetadata,pSet-method Man page
get.amino.acids Man page Source code
get.atomic.mass Man page Source code
getBpParam Source code
getCacheEnv Source code
getClassVersion Source code
getClassVersionString Source code
getColsFromPattern Source code
getCurveWidth Source code
getEcols Man page Source code
getRowsFromPattern Source code
getVariableName Man page Source code
grepEcols Man page Source code
hasChromatograms Man page Source code
hasSpectra Man page Source code
header Man page
header,OnDiskMSnExp,missing-method Man page
header,OnDiskMSnExp,numeric-method Man page
header,pSet,missing-method Man page
header,pSet,numeric-method Man page
iPQF Man page Source code
iPQF.method Source code
iTRAQ4 Man page
iTRAQ5 Man page
iTRAQ8 Man page
iTRAQ9 Man page
idSummary Man page
idSummary,MSnExp-method Man page
idSummary,MSnSet-method Man page
image,MSnSet-method Man page
image2 Man page Source code
imageNA2 Man page Source code
imp_neighbour_avg Source code
impute Man page
impute,MSnSet-method Man page
impute-methods Man page
imputeMethods Man page Source code
injectionTimeFromFile1 Source code
instrumentCustomisations Man page
instrumentCustomisations,MIAPE-method Man page
instrumentCustomisations,pSet-method Man page
instrumentManufacturer Man page
instrumentManufacturer,MIAPE-method Man page
instrumentManufacturer,pSet-method Man page
instrumentModel Man page
instrumentModel,MIAPE-method Man page
instrumentModel,pSet-method Man page
intensity Man page
intensity,Chromatogram-method Man page
intensity,MSpectra-method Man page
intensity,OnDiskMSnExp-method Man page
intensity,Spectrum-method Man page
intensity,pSet-method Man page
ionCount Man page
ionCount,MSpectra-method Man page
ionCount,OnDiskMSnExp-method Man page
ionCount,Spectrum-method Man page
ionCount,pSet-method Man page
ionSource Man page
ionSource,MIAPE-method Man page
ionSource,MSnSet-method Man page
ionSource,pSet-method Man page
ionSourceDetails Man page
ionSourceDetails,MIAPE-method Man page
ionSourceDetails,pSet-method Man page
is.na.MSnSet Man page Source code
isCdfFile Source code
isCentroided Man page
isCentroided,MSnExp-method Man page
isCentroided,MSpectra-method Man page
isCentroided,OnDiskMSnExp-method Man page
isCentroided,Spectrum-method Man page
isCentroidedFromFile Man page Source code
isEmpty,Chromatogram-method Man page
isEmpty,MChromatograms-method Man page
isEmpty,MSpectra-method Man page
isEmpty,Spectrum-method Man page
isEmpty,environment-method Man page
isMSnbaseFastLoad Man page Source code
isMSnbaseVerbose Man page Source code
isOnDisk Source code
isolationWindow,MSnExp-method Man page
isolationWindowLowerMz Man page
isolationWindowLowerMz,OnDiskMSnExp-method Man page
isolationWindowLowerMz,pSet-method Man page
isolationWindowUpperMz Man page
isolationWindowUpperMz,OnDiskMSnExp-method Man page
isolationWindowUpperMz,pSet-method Man page
itraqdata Man page Man page
kNeighbors Source code
lapply,MSnSetList-method Man page
length Man page
length,Chromatogram-method Man page
length,FeaturesOfInterest-method Man page
length,FoICollection-method Man page
length,MSnSetList-method Man page
length,OnDiskMSnExp-method Man page
length,ReporterIons-method Man page
length,pSet-method Man page
length-method Man page
lengths,FoICollection-method Man page
levelIndex Source code
lineplot Source code
list2Spectrum2 Source code
listOf Man page Source code
lockCacheEnv Source code
log,MSnSet-method Man page
logging Source code
makeCamelCase Man page Source code
makeImpuritiesMatrix Man page Source code
makeMTD Man page Source code
makeNaData Man page Source code
makeNaData2 Man page Source code
makePEP Man page Source code
makePRT Man page Source code
makePepMSnSet Source code
makeProtMSnSet Source code
makePsmMSnSet Source code
matchPeaks Source code
meanMzInts Man page Source code
meanSdPlot,MSnSet-method Man page
mergeFeatureVars Man page Source code
metadata,MzTab-method Man page
missing-data Man page
missingdata Man page
moleculeEvidence Man page Source code
moleculeFeatures Man page Source code
ms2df Man page Source code
msInfo Man page
msInfo,MIAPE-method Man page
msInfo,MSnSet-method Man page
msInfo,pSet-method Man page
msInfo_MIAPE Source code
msLevel Man page
msLevel,Chromatogram-method Man page
msLevel,MSmap-method Man page
msLevel,MSpectra-method Man page
msLevel,OnDiskMSnExp-method Man page
msLevel,Spectrum-method Man page
msLevel,pSet-method Man page
msMap Man page
msMap,MSmap-method Man page
msnset Man page
msnset2 Man page
msnsets Man page Source code
multiLabels Man page
multiLabels,NAnnotatedDataFrame-method Man page
multiplex Man page
multiplex,NAnnotatedDataFrame-method Man page
mz Man page
mz,Chromatogram-method Man page
mz,MChromatograms-method Man page
mz,MSmap-method Man page
mz,MSpectra-method Man page
mz,OnDiskMSnExp-method Man page
mz,ReporterIons-method Man page
mz,Spectrum-method Man page
mz,pSet-method Man page
mzRes Man page
mzRes,MSmap-method Man page
mzTabMode Man page Source code
mzTabType Man page Source code
nFeatures Man page Source code
nQuants Man page Source code
names,FeatComp-method Man page
names,FoICollection-method Man page
names,MSnSetList-method Man page
names,ReporterIons-method Man page
names<-,FoICollection,character-method Man page
names<-,MSnSetList,ANY-method Man page
naplot Man page Source code
naset Man page
navMS Man page Source code
ncol,MSmap-method Man page
nextMS Man page Source code
nologging Source code
normToReference Man page Source code
normalise Man page
normalise,MSnExp-method Man page
normalise,MSnSet-method Man page Man page
normalise,OnDiskMSnExp-method Man page
normalise,Spectrum-method Man page
normalise,Spectrum2-method Man page
normalise-methods Man page
normalise_MSnExp Source code
normalise_MSnSet Source code
normalise_Spectrum Source code
normalize Man page
normalize,MSnExp-method Man page
normalize,MSnSet-method Man page
normalize,OnDiskMSnExp-method Man page
normalize,Spectrum-method Man page
normalize,Spectrum2-method Man page
normalize-methods Man page
notes,MIAPE-method Man page
notes,pSet-method Man page
notes<-,MIAPE-method Man page
npcv Man page Source code
nrow,MSmap-method Man page
numberOfCommonPeaks Source code
objlog Man page Source code
otherInfo,MIAPE-method Man page
pData,MChromatograms-method Man page
pData,pSet-method Man page
pData<-,MChromatograms,data.frame-method Man page
pData<-,MSnSet,data.frame-method Man page
pData<-,pSet,ANY-method Man page
pSet Man page
pSet-class Man page
peaksAsLists Source code
peaksCount Man page
peaksCount,MSpectra,ANY-method Man page
peaksCount,OnDiskMSnExp,missing-method Man page
peaksCount,OnDiskMSnExp,numeric-method Man page
peaksCount,Spectrum,missing-method Man page
peaksCount,pSet,missing-method Man page
peaksCount,pSet,numeric-method Man page
peptides,MzTab-method Man page
phenoData,MChromatograms-method Man page
phenoData,pSet-method Man page
phenoData<-,pSet,ANY-method Man page
pickPeaks Man page
pickPeaks,MSnExp-method Man page Man page
pickPeaks,MSpectra-method Man page
pickPeaks,OnDiskMSnExp-method Man page
pickPeaks,Spectrum-method Man page Man page
pickPeaks-methods Man page
pickPeaks_MSnExp Source code
pickPeaks_Spectrum Source code
plot Man page
plot,Chromatogram,ANY-method Man page
plot,MChromatograms,ANY-method Man page
plot,MSmap,missing-method Man page
plot,MSnExp Man page
plot,MSnExp,missing-method Man page
plot,Spectrum,Spectrum-method Man page
plot,Spectrum,missing-method Man page
plot,Spectrum-method Man page
plot,Spectrum2,character-method Man page
plot-methods Man page
plot.MSnExp Man page
plot.Spectrum Man page
plot.Spectrum.Spectrum Man page
plot.Spectrum.character Man page
plot2d Man page
plot2d,MSnExp-method Man page
plot2d,data.frame-method Man page
plot2d-methods Man page
plot2d.header Source code
plot3D Man page
plot3D,MSmap-method Man page
plotDensity Man page
plotDensity,MSnExp-method Man page
plotDensity,data.frame-method Man page
plotDensity-methods Man page
plotDensity.header Source code
plotMzDelta Man page
plotMzDelta,MSnExp-method Man page
plotMzDelta,mzRramp-method Man page
plotMzDelta-methods Man page
plotMzDelta_MSnExp Source code
plotMzDelta_list Source code
plotNA Man page
plotNA,MSnSet-method Man page
plotNA,matrix-method Man page
plotNA-methods Man page
plotNA_matrix Source code
plotSpectrumVsSpectrum Source code
plotXIC_MSnExp Source code
plot_MSnExp Source code
plot_Spectrum1 Source code
plot_Spectrum2 Source code
polarity Man page
polarity,MChromatograms-method Man page
polarity,MSpectra-method Man page
polarity,OnDiskMSnExp-method Man page
polarity,Spectrum-method Man page
polarity,pSet-method Man page
precAcquisitionNum Man page
precAcquisitionNum,Spectrum-method Man page
precAcquisitionNum,pSet-method Man page
precScanNum Man page
precScanNum,MSpectra-method Man page
precScanNum,OnDiskMSnExp-method Man page Man page
precScanNum,Spectrum-method Man page
precScanNum,pSet-method Man page
precSelection Man page Source code
precSelectionTable Man page Source code
precursorCharge Man page
precursorCharge,MSpectra-method Man page
precursorCharge,OnDiskMSnExp-method Man page
precursorCharge,Spectrum-method Man page
precursorCharge,pSet-method Man page
precursorIntensity Man page
precursorIntensity,MSpectra-method Man page
precursorIntensity,OnDiskMSnExp-method Man page
precursorIntensity,Spectrum-method Man page
precursorIntensity,pSet-method Man page
precursorMz Man page
precursorMz,Chromatogram-method Man page
precursorMz,MChromatograms-method Man page
precursorMz,MSpectra-method Man page
precursorMz,OnDiskMSnExp-method Man page
precursorMz,Spectrum-method Man page
precursorMz,pSet-method Man page
precursorValue_OnDiskMSnExp Source code
prevMS Man page Source code
processingData Man page
processingData,MSnSet-method Man page
processingData,pSet-method Man page
processingQueue Source code
productMz Man page
productMz,Chromatogram-method Man page
productMz,MChromatograms-method Man page
proteins,MzTab-method Man page
protocolData,pSet-method Man page
psms,MzTab-method Man page
pubMedIds,MIAPE-method Man page
pubMedIds,pSet-method Man page
pubMedIds<-,MIAPE-method Man page
purityCorrect Man page
purityCorrect,MSnSet,matrix-method Man page
purityCorrect,MSnSet-method Man page
purityCorrect-methods Man page
qual Man page
qual,MSnSet-method Man page
quantify Man page
quantify,MSnExp,character-method Man page
quantify,MSnExp-method Man page
quantify,OnDiskMSnExp-method Man page
quantify,OnMSnExp-method Man page
quantify,Spectrum,character-method Man page
quantify,Spectrum-method Man page
quantify-methods Man page
quantify_MSnExp Source code
quantify_OnDiskMSnExp_max Source code
quantify_Spectrum Source code
ratio.mat Source code
ratios,MSnSet-method Man page
readInMemMSData Source code
readMSData Man page Source code
readMSData2 Man page Source code
readMSnSet Man page Source code
readMSnSet2 Man page Source code
readMgfData Man page Source code
readMzIdData Man page Source code
readMzTabData Man page Source code
readMzTabData_v0.9 Man page Source code
readMzXMLData Man page Source code
readOnDiskMSData Source code
readSRMData Man page Source code
reduce,data.frame-method Man page
redundant.dist Source code
relaxedMatch Source code
removeMultipleAssignment Man page
removeMultipleAssignment,MSnExp-method Man page
removeMultipleAssignment,MSnSet-method Man page
removeMultipleAssignment-method Man page
removeNoId Man page
removeNoId,MSnExp-method Man page
removeNoId,MSnSet-method Man page
removeNoId-methods Man page
removePeaks Man page
removePeaks,MSnExp-method Man page Man page
removePeaks,MSpectra-method Man page
removePeaks,OnDiskMSnExp-method Man page
removePeaks,Spectrum-method Man page Man page
removePeaks-methods Man page
removePeaks_MSnExp Source code
removePeaks_Spectrum Source code
removeReporters Man page
removeReporters,MSnExp-method Man page
removeReporters,OnDiskMSnExp-method Man page
removeReporters,Spectrum-method Man page
removeReporters-methods Man page
removeReporters_MSnExp Source code
removeReporters_Spectrum2 Source code
reporterColors Man page
reporterColors,ReporterIons-method Man page
reporterColors-method Man page
reporterColours Man page
reporterColours,ReporterIons-method Man page
reporterColours-method Man page
reporterNames Man page
reporterNames,ReporterIons-method Man page
reporterNames-method Man page
reporterNames<- Man page
reporterNames<-,ReporterIons,ANY-method Man page
reporterNames<-,ReporterIons,character-method Man page
reporterNames<-,ReporterIons-method Man page
requiredFvarLabels Man page Source code
reshapeMetadata Source code
rmFeaturesOfInterest Man page
rmFeaturesOfInterest,FoICollection,numeric-method Man page
rmFeaturesOfInterest-methods Man page
robustSummary Source code
rowmean Source code
rownames<-,MChromatograms-method Man page
rowsd Source code
rtime Man page
rtime,Chromatogram-method Man page
rtime,MSmap-method Man page
rtime,MSpectra-method Man page
rtime,OnDiskMSnExp-method Man page
rtime,Spectrum-method Man page
rtime,pSet-method Man page
sampleNames,MChromatograms-method Man page
sampleNames,pSet-method Man page
sampleNames<-,MChromatograms,ANY-method Man page
sampleNames<-,pSet,character-method Man page
samples,MIAPE-method Man page
sapply,MSnSetList-method Man page
scale,MSnSet-method Man page
scanIndex Man page
scanIndex,MSpectra-method Man page
scanIndex,OnDiskMSnExp-method Man page
scanIndex,Spectrum-method Man page
scanIndex,pSet-method Man page
selectFeatureData Man page Source code
setCacheEnv Source code
setMSnbaseFastLoad Man page Source code
setMSnbaseParallelThresh Man page Source code
setMSnbaseVerbose Man page Source code
show,Chromatogram-method Man page
show,FeatComp-method Man page
show,FeaturesOfInterest-method Man page
show,FoICollection-method Man page
show,MChromatograms-method Man page
show,MIAPE-method Man page
show,MSmap-method Man page
show,MSnExp-method Man page
show,MSnProcess-method Man page
show,MSnSet-method Man page
show,MSnSetList-method Man page
show,MSpectra-method Man page
show,MzTab-method Man page
show,NAnnotatedDataFrame-method Man page
show,OnDiskMSnExp-method Man page
show,ProcessingStep-method Man page
show,ReporterIons-method Man page
show,Spectrum-method Man page
show_MIAPE Source code
show_MSnProcess Source code
show_ReporterIons Source code
show_Spectrum1 Source code
show_Spectrum2 Source code
smallMolecules Man page Source code
smooth Man page
smooth,MSnExp-method Man page Man page
smooth,MSpectra-method Man page
smooth,OnDiskMSnExp-method Man page
smooth,Spectrum-method Man page Man page
smooth-methods Man page
smooth_MSnExp Source code
smooth_Spectrum Source code
smoothed Man page
smoothed,MSpectra-method Man page
smoothed,OnDiskMSnExp-method Man page
smoothed,Spectrum-method Man page
smoothed,pSet-method Man page
smoothed<- Man page
smoothed<-,OnDiskMSnExp,logical-method Man page
smoothed<-,Spectrum,ANY-method Man page
smoothed<-,Spectrum,logical-method Man page
smoothed<-,pSet,ANY-method Man page
smoothed<-,pSet,logical-method Man page
spectra Man page
spectra,MSnExp-method Man page
spectra,OnDiskMSnExp-method Man page
spectra,pSet-method Man page
spectrapply Man page
spectrapply,OnDiskMSnExp-method Man page
spectrapply,pSet-method Man page
split,MSnSet,character-method Man page
split,MSnSet,factor-method Man page
splitByFile Man page
splitByFile,MSnExp,factor-method Man page
splitByFile,OnDiskMSnExp,factor-method Man page
subsetFeatureDataBy Source code
t,MSmap-method Man page
t.MSnSet Man page Source code
testCacheArg Source code
tic Man page
tic,MSpectra-method Man page
tic,OnDiskMSnExp-method Man page
tic,Spectrum-method Man page
tic,pSet-method Man page
tic_MSnSet Source code
topN Man page
topN,MSnSet,MSnSet-method Man page
topN,MSnSet-method Man page
topN,matrix-method Man page
trimMz Man page
trimMz,MSnExp,numeric-method Man page
trimMz,MSnExp-method Man page Man page
trimMz,OnDiskMSnExp,numeric-method Man page
trimMz,Spectrum,numeric-method Man page
trimMz,Spectrum-method Man page Man page
trimMz-methods Man page
trimMz_Spectrum Source code
trimws Man page
trimws,MSnSet-method Man page
trimws,data.frame-method Man page
uni.measured.dist Source code
unique1 Man page
unique1,FeatComp-method Man page
unique1,methods Man page
unique2 Man page
unique2,FeatComp-method Man page
unique2,methods Man page
uniques.list Source code
unsplit,MSnSetList,factor-method Man page
updateFeatureNames Man page Source code
updateFvarLabels Man page Source code
updateMSnExp Source code
updateObject,MSnExp-method Man page
updateObject,Spectrum-method Man page
updateSampleNames Man page Source code
updateSpectrum2 Source code
utils.clean Source code
utils.enableNeighbours Source code
utils.getMzDelta Source code
utils.idSummary Source code
utils.leftJoin Source code
utils.list2ssv Source code
utils.mergeSpectraAndIdentificationData Source code
utils.removeMultipleAssignment Source code
utils.removeNoId Source code
utils.removeNoIdAndMultipleAssignments Source code
utils.removePeaks Source code
utils.removePeaks_centroided Source code
utils.removePrecMz Source code
utils.removePrecMz_Spectrum Source code
utils.removePrecMz_list Source code
utils.ssv2list Source code
utils.ssv2vec Source code
utils.vec2ssv Source code
utils.vec2ssv.data.frame Source code
validSpectrum Source code
validateFeatureDataForOnDiskMSnExp Source code
validateOnDiskMSnExp Man page Source code
varLabels,pSet-method Man page
varMetadata,pSet-method Man page
whichNA Man page Source code
width Man page
width,ReporterIons-method Man page
width-method Man page
windowIndices Source code
write.exprs Man page
write.exprs,MSnSet-method Man page
writeMSData Man page
writeMSData,MSnExp,character-method Man page
writeMgfContent Source code
writeMgfData Man page
writeMgfData,MSnExp-method Man page
writeMgfData,MSpectra-method Man page
writeMgfData,Spectrum-method Man page
writeMgfData-methods Man page
writeMgfDataFile Source code
writeMzTabData Man page Source code
zoom Source code
MSnbase documentation built on Jan. 23, 2021, 2 a.m.

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