MSnbase: Base Functions and Classes for Mass Spectrometry and Proteomics
Version 2.2.0

Manipulation, processing and visualisation of mass spectrometry and proteomics data.

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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.
Bioconductor views DataImport Infrastructure MassSpectrometry Proteomics QualityControl
Date of publicationNone
MaintainerLaurent Gatto <lg390@cam.ac.uk>
LicenseArtistic-2.0
Version2.2.0
URL https://github.com/lgatto/MSnbase
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("MSnbase")

Man pages

addIdentificationData-methods: Adds Identification Data
aggvar: Identify aggregation outliers
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
navMS: Navigate an 'MSnExp' object
nFeatures: How many features in a group?
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

Functions

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
MIAPE Man page
MIAPE-class Man page
MSmap Man page Source code
MSmap-class 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 Man page
MSnbase-defunct Man page
MSnbase-deprecated Man page
MSnbase-package Man page
MSnbaseOptions Man page Source code
MzTab Man page Source code
MzTab-class Man page
NAnnotatedDataFrame Man page
NAnnotatedDataFrame-class 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
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
[,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
[[,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,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,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-methods Man page
addMzTabMetadata 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
applyFun2SpectraOfFileMulti Source code
applyFun2SpectraOfFileSingle Source code
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.MSmap Source code
as.data.frame.MSnSet Man page Source code
as.data.frame.Spectrum 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,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
breaks_Spectra Source code
breaks_Spectrum Source code
cacheEnvIsLocked Source code
calcCompNumbers Source code
calculateFragments Man page Source code
calculateFragments,character,Spectrum2-method Man page
calculateFragments,character,missing-method Man page
calculateFragments_Spectrum2 Source code
centroided 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 Source code
chromatogram,character-method Man page
chromatogram,data.frame-method Man page
chromatogram,mzRramp-method Man page
chromatogram-methods 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,MSnExp-method Man page 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,ExpressionSet,MSnSet-method Man page
coerce,FoICollection,matrix-method Man page
coerce,IBSpectra,MSnSet-method Man page
coerce,MIAPE,MIAME-method Man page
coerce,MSmap,data.frame-method Man page
coerce,MSnSet,ExpressionSet-method Man page
coerce,MSnSet,data.frame-method Man page
coerce,MzTab,MSnSetList-method Man page
coerce,OnDiskMSnExp,MSnExp-method Man page
coerce,Spectrum,data.frame-method Man page
collisionEnergy Man page
collisionEnergy,OnDiskMSnExp-method Man page
collisionEnergy,Spectrum-method Man page
collisionEnergy,pSet-method Man page
combine,MIAPE,MIAPE-method Man page
combine,MSnProcess,MSnProcess-method Man page
combine,MSnSet,MSnSet-method Man page
combineFeatures Man page Source code
combineFeaturesL Source code
combineFeaturesV Source code
combineMatrixFeatures 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
compStrings 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
countAndPrint Source code
count_MSnSet Source code
cramer4 Source code
curveData Source code
curveStats_Spectrum Source code
defaultNeutralLoss Man page 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
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
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
exprsToRatios Man page
exprsToRatios,MSnSet-method Man page
exprsToRatios,matrix-method Man page
exprsToRatios-methods 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
fData,pSet-method Man page
fData<-,pSet,data.frame-method Man page
fastquant_max Source code
featureCV Man page Source code
featureData,pSet-method Man page
featureNames,OnDiskMSnExp-method Man page
featureNames,pSet-method Man page
featureNames<-,OnDiskMSnExp,ANY-method Man page
featureNames<-,OnDiskMSnExp-method Man page
fileExt Source code
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
filterEmptySpecetra,MSnExp-method Man page
filterEmptySpecetra,OnDiskMSnExp-method Man page
filterEmptySpectra Man page
filterFile Man page
filterFile,MSnExp-method Man page
filterFile,OnDiskMSnExp-method Man page
filterMsLevel Man page
filterMsLevel,MSnExp-method Man page
filterMsLevel,OnDiskMSnExp-method Man page
filterMz Man page
filterMz,MSnExp-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
filterRt 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
firstMsLevel Source code
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
formatRt Man page Source code
fromFile Man page
fromFile,OnDiskMSnExp-method Man page
fromFile,Spectrum-method Man page
fromFile,pSet-method Man page
fvarLabels,pSet-method Man page
fvarMetadata,pSet-method Man page
get.amino.acids Man page Source code Source code
get.atomic.mass Man page Source code 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
getRatios Man page Source code
getRowsFromPattern Source code
getVariableName Man page Source code
grepEcols Man page Source code
header Man page Source code
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,OnDiskMSnExp-method Man page
intensity,Spectrum-method Man page
intensity,pSet-method Man page
ionCount 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,OnDiskMSnExp-method Man page
isCentroided,Spectrum-method Man page
isEmpty,Spectrum-method Man page
isEmpty,environment-method Man page
isMSnbaseVerbose Man page Source code
isOnDisk Source code
isolationWindow,MSnExp-method Man page
itraqdata Man page Man page
lapply,MSnSetList-method Man page
length 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
lineplot Source code
list2Spectrum2 Source code
listOf Man page Source code
lockCacheEnv Source code
log,MSnSet-method Man page
logging 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
meanSdPlot,MSnSet-method Man page
metadata,MzTab-method Man page
missing-data Man page
missingdata Man page
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,MSmap-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,MSmap-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
neutralLoss Source code
nextMS Man page Source code
nologging Source code
normToReferenceFraction 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
onAttach Source code
onLoad Source code
otherInfo,MIAPE-method Man page
pData,pSet-method Man page
pSet Man page
pSet-class Man page
peaksAsLists Source code
peaksCount 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,pSet-method Man page
pickPeaks Man page
pickPeaks,MSnExp-method Man page 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,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
plotSingleSpectrum Source code
plotSpectrumVsSpectrum Source code Source code
plot_MSnExp Source code
plot_OnDiskMSnExp Source code
plot_Spectrum1 Source code
plot_Spectrum2 Source code
polarity 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,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,OnDiskMSnExp-method Man page
precursorCharge,Spectrum-method Man page
precursorCharge,pSet-method Man page
precursorIntensity Man page
precursorIntensity,OnDiskMSnExp-method Man page
precursorIntensity,Spectrum-method Man page
precursorIntensity,pSet-method Man page
precursorMz Man page
precursorMz,OnDiskMSnExp-method Man page
precursorMz,Spectrum-method Man page
precursorMz,pSet-method Man page
precursorValue_OnDiskMSnExp Source code
preparePlotNAData Source code
prevMS Man page Source code
processingData Man page
processingData,MSnSet-method Man page
processingData,pSet-method Man page
processingQueue Source code
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
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
readMzTabData Man page Source code
readMzTabData_v0.9 Man page Source code
readMzXMLData Man page Source code
redundant.dist Source code
referenceFraction 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,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
reshapeMetadata Source code
rmFeaturesOfInterest Man page
rmFeaturesOfInterest,FoICollection,numeric-method Man page
rmFeaturesOfInterest-methods Man page
rowMaxs Source code
rtime Man page
rtime,MSmap-method Man page
rtime,OnDiskMSnExp-method Man page
rtime,Spectrum-method Man page
rtime,pSet-method Man page
sCentroided Source code
sCentroidedFromFile Source code
sameNbCol Source code
sameNbRow Source code
sampleNames,pSet-method Man page
sampleNames<-,pSet,character-method Man page
samples,MIAPE-method Man page
scale,MSnSet-method Man page
scanIndex Man page
scanIndex,OnDiskMSnExp-method Man page
scanIndex,Spectrum-method Man page
scanIndex,pSet-method Man page
selectFeatureData Man page Source code
selectShinyFeatureData Source code
selectTextFeatureData Source code
setCacheEnv Source code
setMSnbaseParallelThresh Man page Source code
setMSnbaseVerbose Man page Source code
show,FeatComp-method Man page
show,FeaturesOfInterest-method Man page
show,FoICollection-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,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.ReporterIons Source code
show_MIAPE Source code
show_MSnProcess Source code
show_Spectrum1 Source code
show_Spectrum2 Source code
slotNames0 Source code
smallMolecules Man page Source code
smooth Man page
smooth,MSnExp-method Man page 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,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
subsetFeatureDataBy Source code
summariseRows Source code
t,MSmap-method Man page
t.MSnSet Man page Source code
terminalModifications Source code
testCacheArg Source code
testReadMSDataInput Source code
tic Man page
tic,OnDiskMSnExp-method Man page
tic,Spectrum-method Man page
tic,pSet-method Man page
tic_MSnSet Source code
topIdx 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
trimws.useAsDefault Source code
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.applyColumnwiseByGroup Source code
utils.clean Source code
utils.colSd Source code
utils.getMzDelta Source code
utils.getMzDelta_list 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_list Source code
utils.ssv2list Source code
utils.ssv2vec Source code
utils.vec2ssv Source code
validSpectrum Source code
validateFeatureDataForOnDiskMSnExp Source code
validateOnDiskMSnExp Man page Source code
varLabels,pSet-method Man page
varMetadata,pSet-method Man page
versionToNum Source code
whichNA Man page Source code
width Man page
width,ReporterIons-method Man page
width-method Man page
write.exprs Man page
write.exprs,MSnSet-method Man page
writeMgfContent Source code
writeMgfData Man page
writeMgfData,MSnExp-method Man page
writeMgfData,Spectrum-method Man page
writeMgfData-methods Man page
writeMgfDataFile Source code
writeMzTabData Man page Source code
xic Man page
xic,character-method Man page
xic,mzRramp-method Man page
xic-methods Man page
xic_1 Source code
xicplot Source code
zoom Source code

Files

.Rinstignore
CONDUCT.md
DESCRIPTION
NAMESPACE
NEWS
R
R/AllClassUnions.R
R/AllGenerics.R
R/DataClasses.R
R/MzTab.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-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-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-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.md
build
build/vignette.rds
data
data/TMT10.RData
data/TMT10ETD.RData
data/TMT10HCD.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
inst/CITATION
inst/doc
inst/doc/MSnbase-demo
inst/doc/MSnbase-demo.R
inst/doc/MSnbase-demo.Rnw
inst/doc/MSnbase-demo.pdf
inst/doc/MSnbase-development
inst/doc/MSnbase-development.R
inst/doc/MSnbase-development.Rmd
inst/doc/MSnbase-development.html
inst/doc/MSnbase-io
inst/doc/MSnbase-io.R
inst/doc/MSnbase-io.Rmd
inst/doc/MSnbase-io.html
inst/doc/benchmarking.R
inst/doc/benchmarking.Rmd
inst/doc/benchmarking.html
inst/extdata
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
inst/scripts/benchmarking.R
inst/scripts/make_msx.R
inst/scripts/naset.R
inst/scripts/torture.R
inst/tests
man
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-methods.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/featureCV.Rd
man/fillUp.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/makeNaData.Rd
man/missing-data.Rd
man/nFeatures.Rd
man/nQuants.Rd
man/naplot.Rd
man/navMS.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/readMzTabData.Rd
man/readMzTabData_v0.9.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
man/xic-methods.Rd
src
src/MSnbase.h
src/RcppExports.cpp
src/Spectrum1_class.c
src/Spectrum2_class.c
src/imp_neighbour_avg.cpp
src/utils.c
tests
tests/testthat
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_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_iPQF.R
tests/testthat/test_impute.R
tests/testthat/test_io.R
tests/testthat/test_matching.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_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
vignettes/Bugs.md
vignettes/Bugs.tex
vignettes/Figures
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/itraqchem.pdf
vignettes/Figures/msnset.png
vignettes/Figures/plot2d-figure.png
vignettes/Figures/plotDensity-figure.png
vignettes/Figures/plotMzDelta-pride12011.pdf
vignettes/Figures/tmt10comp.pdf
vignettes/Foreword.md
vignettes/Foreword.tex
vignettes/MSnbase-demo.Rnw
vignettes/MSnbase-development.Rmd
vignettes/MSnbase-io.Rmd
vignettes/MSnbase.bib
vignettes/benchmarking.Rmd
MSnbase documentation built on May 20, 2017, 9:23 p.m.