MSnbase: Base Functions and Classes for MS-based Proteomics

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

AuthorLaurent Gatto <lg390@cam.ac.uk> with contributions from Guangchuang Yu, Samuel Wieczorek, Vasile-Cosmin Lazar, Vladislav Petyuk, Thomas Naake, Richie Cotton, Martina Fisher, Johannes Rainer and Sebastian Gibb.
Date of publicationNone
MaintainerLaurent Gatto <lg390@cam.ac.uk>
LicenseArtistic-2.0
Version2.0.2
https://github.com/lgatto/MSnbase

View on Bioconductor

Man pages

addIdentificationData-methods: Adds Identification Data

averageMSnSet: Generate an average 'MSnSet'

bin-methods: Bin 'MSnExp' or 'Spectrum' instances

calculateFragments-methods: Calculate ions produced by fragmentation.

chromatogram-methods: Plots a chromatogram

clean-methods: Cleans 'MSnExp' or 'Spectrum' instances

combineFeatures: Combines features in an 'MSnSet' object

commonFeatureNames: Keep only common feature names

compareMSnSets: Compare two MSnSets

compareSpectra-methods: Compare Spectra of an 'MSnExp' or 'Spectrum' instances

defunct: MSnbase Deprecated and Defunct

estimateNoise-method: Noise Estimation for 'Spectrum' instances

exprsToRatios-methods: Calculate all ratio pairs

extractPrecSpectra-methods: Extracts precursor-specific spectra from an 'MSnExp' object

FeatComp-class: Class '"FeatComp"'

featureCV: Calculates coeffivient of variation for features

FeaturesOfInterest-class: Features of Interest

fillUp: Fills up a vector

formatRt: Format Retention Time

get.amino.acids: Amino acids

get.atomic.mass: Atomic mass.

getVariableName: Return a variable name

grepEcols: Returns the matching column names of indices.

imageNA2: NA heatmap visualisation for 2 groups

impute-methods: Quantitative proteomics data imputation

iPQF: iPQF: iTRAQ (and TMT) Protein Quantification based on...

iTRAQ4: iTRAQ 4-plex set

itraqdata: Example 'MSnExp' and 'MSnSet' data sets

listOf: Tests equality of list elements class

makeNaData: Create a data with missing values

MIAPE-class: The "MIAPE" Class for Storing Proteomics Experiment...

missing-data: Documenting missing data visualisation

MSmap-class: Class 'MSmap'

MSnbaseOptions: MSnbase options

MSnbase-package: MSnbase: Base Functions and Classes for MS-based Proteomics

MSnExp-class: The 'MSnExp' Class for MS Data And Meta-Data

MSnProcess-class: The "MSnProcess" Class

MSnSet-class: The "MSnSet" Class for MS Proteomics Expression Data and...

MSnSetList-class: Storing multiple related MSnSets

MzTab-class: Parse 'MzTab' files

NAnnotatedDataFrame-class: Class Containing Measured Variables and Their Meta-Data...

naplot: Overview of missing value

normalise-methods: Normalisation of 'MSnExp', 'MSnSet' and 'Spectrum' objects

npcv: Non-parametric coefficient of variation

nQuants: Count the number of quantitfied features.

OnDiskMSnExp-class: The 'OnDiskMSnExp' Class for MS Data And Meta-Data

pickPeaks-method: Peak Detection for 'MSnExp' or 'Spectrum' instances

plot2d-methods: The 'plot2d' method for 'MSnExp' quality assessment

plotDensity-methods: The 'plotDensity' method for 'MSnExp' quality assessment

plot-methods: Plotting 'Spectrum' object(s)

plotMzDelta-methods: The delta m/z plot

plotNA-methods: Exploring missing data in 'MSnSet' instances

plotSpectrumSpectrum-methods: Plotting a 'Spectrum' vs another 'Spectrum' object.

precSelection: Number of precursor selection events

ProcessingStep-class: Simple processing step class

pSet-class: Class to Contain Raw Mass-Spectrometry Assays and...

purityCorrect-methods: Performs reporter ions purity correction

quantify-methods: Quantifies 'MSnExp' and 'Spectrum' objects

readMgfData: Import mgf files as 'MSnExp' instances.

readMSData: Imports mass-spectrometry raw data files as 'MSnExp'...

readMSnSet: Read 'MSnSet'

readMzTabData: Read an 'mzTab' file

readMzTabData_v0.9: Read an 'mzTab' file

removeNoId-methods: Removes non-identified features

removePeaks-methods: Removes low intensity peaks

removeReporters-methods: Removes reporter ion tag peaks

ReporterIons-class: The "ReporterIons" Class

selectFeatureData: Select feature variables of interest

smooth-methods: Smooths 'MSnExp' or 'Spectrum' instances

Spectrum1-class: The "Spectrum1" Class for MS1 Spectra

Spectrum2-class: The "Spectrum2" Class for MSn Spectra

Spectrum-class: The "Spectrum" Class

TMT6: TMT 6/10-plex sets

trimMz-methods: Trims 'MSnExp' or 'Spectrum' instances

updateObject-methods: Update MSnbase objects

writeMgfData-methods: Write an experiment or spectrum to an mgf file

xic-methods: Extracted ion chromatograms

Functions

abstract,MIAPE-method Man page
abstract,pSet-method Man page
acquisitionNum Man page
acquisitionNum,OnDiskMSnExp-method Man page
acquisitionNum,pSet-method Man page
acquisitionNum,Spectrum-method Man page
addFeaturesOfInterest Man page
addFeaturesOfInterest,FeaturesOfInterest,FoICollection-method Man page
addFeaturesOfInterest-methods Man page
addIdentificationData Man page
addIdentificationData-methods Man page
addIdentificationData,MSnExp,character-method Man page
addIdentificationData,MSnExp,data.frame-method Man page
addIdentificationData,MSnExp,mzIDClasses-method Man page
addIdentificationData,MSnExp,mzIDCollection-method Man page
addIdentificationData,MSnExp,mzID-method Man page
addIdentificationData,MSnSet,character-method Man page
addIdentificationData,MSnSet,data.frame-method Man page
addIdentificationData,MSnSet,mzIDClasses-method Man page
addIdentificationData,MSnSet,mzIDCollection-method Man page
addIdentificationData,MSnSet,mzID-method Man page
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
analyserDetails Man page
analyserDetails,MIAPE-method Man page
analyserDetails,pSet-method Man page
analyser,MIAPE-method Man page
analyser,MSnSet-method Man page
analyser,pSet-method Man page
analyzer Man page
analyzerDetails Man page
analyzerDetails,MIAPE-method Man page
analyzerDetails,pSet-method Man page
analyzer,MIAPE-method Man page
analyzer,MSnSet-method Man page
analyzer,pSet-method Man page
as.data.frame.MSnSet Man page
as.data.frame.Spectrum Man page
as.ExpressionSet.MSnSet Man page
as.matrix.FoICollection Man page
as.MIAME.MIAPE Man page
as.MSnExp.OnDiskMSnExp Man page
as.MSnSet.ExpressionSet Man page
assayData,OnDiskMSnExp-method Man page
assayData,pSet-method Man page
averageMSnSet Man page
bin Man page
bin-methods Man page
bin,MSnExp-method Man page
bin,MSnExp-method Man page
bin,OnDiskMSnExp-method Man page
bin,Spectrum-method Man page
bin,Spectrum-method Man page
calculateFragments Man page
calculateFragments,character,missing-method Man page
calculateFragments,character,Spectrum2-method Man page
centroided Man page
centroided<- Man page
centroided<-,OnDiskMSnExp,logical-method Man page
centroided,OnDiskMSnExp-method Man page
centroided<-,pSet,ANY-method Man page
centroided<-,pSet,logical-method Man page
centroided,pSet-method Man page
centroided<-,Spectrum,ANY-method Man page
centroided<-,Spectrum,logical-method Man page
centroided,Spectrum-method Man page
chromatogram Man page
chromatogram,character-method Man page
chromatogram,data.frame-method Man page
chromatogram-methods Man page
chromatogram,mzRramp-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:pSet Man page
class:ReporterIons Man page
class:Spectrum Man page
class:Spectrum1 Man page
class:Spectrum2 Man page
clean Man page
clean-methods Man page
clean,MSnExp-method Man page
clean,MSnExp-method Man page
clean,OnDiskMSnExp-method Man page
clean,Spectrum-method Man page
clean,Spectrum-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,MSmap,data.frame-method Man page
coerce,MSnSet,data.frame-method Man page
coerce,MSnSet,ExpressionSet-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,pSet-method Man page
collisionEnergy,Spectrum-method Man page
combineFeatures Man page
combine,MIAPE,MIAPE-method Man page
combine,MSnProcess,MSnProcess-method Man page
combine,MSnSet,MSnSet-method Man page
comments Man page
common Man page
common,FeatComp-method Man page
commonFeatureNames Man page
common,methods Man page
compareMSnSets Man page
compareSpectra Man page
compareSpectra-methods Man page
compareSpectra,MSnExp-method Man page
compareSpectra,MSnExp,missing-method Man page
compareSpectra,OnDiskMSnExp,missing-method Man page
compareSpectra,Spectrum-method Man page
compareSpectra,Spectrum,Spectrum-method Man page
compfnames Man page
compfnames,list,missing-method Man page
compfnames-methods Man page
compfnames,MSnSet,MSnSet-method Man page
defaultNeutralLoss Man page
description,FeaturesOfInterest-method Man page
description,FoICollection-method Man page
description,MSnSet-method Man page
description,pSet-method Man page
description,ReporterIons-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
droplevels.MSnSet Man page
estimateNoise Man page
estimateNoise-methods Man page
estimateNoise,MSnExp-method Man page
estimateNoise,OnDiskMSnExp-method Man page
estimateNoise,Spectrum-method Man page
executeProcessingStep Man page
expemail Man page
expemail,MIAPE-method Man page
expemail,MSnSet-method Man page
expemail,pSet-method Man page
experimentData<-,MSnSet,MIAPE-method Man page
experimentData,pSet-method Man page
expinfo,MIAPE-method Man page
exprs,MSnSet-method Man page
exprsToRatios Man page
exprsToRatios,matrix-method Man page
exprsToRatios-methods Man page
exprsToRatios,MSnSet-method Man page
exptitle Man page
exptitle,MIAPE-method Man page
exptitle,MSnSet-method Man page
exptitle,pSet-method Man page
extractPrecSpectra Man page
extractPrecSpectra-methods Man page
extractPrecSpectra,MSnExp-method Man page
extractPrecSpectra,MSnExp,numeric-method Man page
extractPrecSpectra,OnDiskMSnExp,numeric-method Man page
extractSpectra Man page
extractSpectra,MSnExp,logical-method Man page
extractSpectra,MSnExp-method Man page
fData<-,pSet,data.frame-method Man page
fData,pSet-method Man page
FeatComp-class Man page
featureCV Man page
featureData,pSet-method Man page
featureNames<-,OnDiskMSnExp,ANY-method Man page
featureNames<-,OnDiskMSnExp-method Man page
featureNames,OnDiskMSnExp-method Man page
featureNames,pSet-method Man page
FeaturesOfInterest Man page
FeaturesOfInterest,character,character,missing-method Man page
FeaturesOfInterest,character,character,MSnSet-method Man page
FeaturesOfInterest-class Man page
FeaturesOfInterest-methods 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
filterAcquisitionNum Man page
filterAcquisitionNum,MSnExp-method Man page
filterAcquisitionNum,OnDiskMSnExp-method 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-methods Man page
filterMz,MSnExp-method Man page
filterMz,OnDiskMSnExp-method Man page
filterMz,Spectrum-method Man page
filtermz,Spectrum,numeric-method Man page
filterNA Man page
filterNA,matrix-method Man page
filterNA,MSnSet-method Man page
filterRt Man page
filterRt,MSnExp-method Man page
filterRt,OnDiskMSnExp-method Man page
filterZero Man page
filterZero,matrix-method Man page
filterZero,MSnSet-method Man page
fnamesIn Man page
fnamesIn,FeaturesOfInterest,data.frame-method Man page
fnamesIn,FeaturesOfInterest,matrix-method Man page
fnamesIn,FeaturesOfInterest,MSnSet-method Man page
fnamesIn-methods Man page
foi Man page
FoICollection Man page
FoICollection-class Man page
FoICollection,list-method Man page
FoICollection-methods Man page
FoICollection,missing-method Man page
foi,FeaturesOfInterest-method Man page
foi,FoICollection-method Man page
foi-methods Man page
formatRt Man page
fromFile Man page
fromFile,OnDiskMSnExp-method Man page
fromFile,pSet-method Man page
fromFile,Spectrum-method Man page
fvarLabels,pSet-method Man page
fvarMetadata,pSet-method Man page
get.amino.acids Man page
get.atomic.mass Man page
getEcols Man page
getRatios Man page
getVariableName Man page
grepEcols Man page
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
idSummary Man page
idSummary,MSnExp-method Man page
idSummary,MSnSet-method Man page
image2 Man page
image,MSnSet-method Man page
imageNA2 Man page
impute Man page
impute-methods Man page
imputeMethods Man page
impute,MSnSet-method Man page
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,pSet-method Man page
intensity,Spectrum-method Man page
ionCount Man page
ionCount,OnDiskMSnExp-method Man page
ionCount,pSet-method Man page
ionCount,Spectrum-method Man page
ionSource Man page
ionSourceDetails Man page
ionSourceDetails,MIAPE-method Man page
ionSourceDetails,pSet-method Man page
ionSource,MIAPE-method Man page
ionSource,MSnSet-method Man page
ionSource,pSet-method Man page
iPQF Man page
isCentroided Man page
isCentroided,MSnExp-method Man page
isCentroided,OnDiskMSnExp-method Man page
isCentroided,Spectrum-method Man page
isEmpty,environment-method Man page
isEmpty,Spectrum-method Man page
isMSnbaseVerbose Man page
is.na.MSnSet Man page
isolationWindow,MSnExp-method Man page
iTRAQ4 Man page
iTRAQ5 Man page
iTRAQ8 Man page
iTRAQ9 Man page
itraqdata Man page
itraqdata Man page
lapply,MSnSetList-method Man page
length Man page
length,FeaturesOfInterest-method Man page
length,FoICollection-method Man page
length-method Man page
length,MSnSetList-method Man page
length,OnDiskMSnExp-method Man page
length,pSet-method Man page
length,ReporterIons-method Man page
lengths,FoICollection-method Man page
listOf Man page
log,MSnSet-method Man page
makeImpuritiesMatrix Man page
makeMTD Man page
makeNaData Man page
makeNaData2 Man page
makePEP Man page
makePRT Man page
MAplot,MSnSet-method Man page
meanSdPlot,MSnSet-method Man page
metadata,MzTab-method Man page
MIAPE Man page
MIAPE-class Man page
missingdata Man page
missing-data Man page
ms2df Man page
msInfo Man page
msInfo,MIAPE-method Man page
msInfo,MSnSet-method Man page
msInfo,pSet-method Man page
msLevel Man page
msLevel,MSmap-method Man page
msLevel,OnDiskMSnExp-method Man page
msLevel,pSet-method Man page
msLevel,Spectrum-method Man page
msMap Man page
MSmap Man page
MSmap-class Man page
msMap,MSmap-method Man page
MSnbase Man page
MSnbase-defunct Man page
MSnbase-deprecated Man page
MSnbaseOptions Man page
MSnbase-package Man page
MSnExp Man page
MSnExp-class Man page
MSnProcess Man page
MSnProcess-class Man page
msnset Man page
MSnSet Man page
msnset2 Man page
[,MSnSet,ANY,ANY,ANY-method Man page
[,MSnSet,ANY,ANY-method Man page
MSnSet-class Man page
MSnSetList Man page
[,MSnSetList,ANY,ANY,ANY-method Man page
[[,MSnSetList,ANY,ANY-method Man page
[[,MSnSetList,ANY,missing-method Man page
[,MSnSetList,ANY,missing,missing-method Man page
MSnSetList-class Man page
[,MSnSet-method Man page
msnsets Man page
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,pSet-method Man page
mz,ReporterIons-method Man page
mzRes Man page
mzRes,MSmap-method Man page
mz,Spectrum-method Man page
MzTab Man page
MzTab-class Man page
mzTabMode Man page
mzTabType Man page
names,FeatComp-method Man page
names<-,MSnSetList,ANY-method Man page
names,MSnSetList-method Man page
names,ReporterIons-method Man page
NAnnotatedDataFrame Man page
NAnnotatedDataFrame-class Man page
naplot Man page
naset Man page
ncol,MSmap-method Man page
normalise Man page
normalise-methods Man page
normalise,MSnExp-method Man page
normalise,MSnSet-method Man page
normalise,MSnSet-method Man page
normalise,OnDiskMSnExp-method Man page
normalise,Spectrum2-method Man page
normalise,Spectrum-method Man page
normalize Man page
normalize-methods Man page
normalize,MSnExp-method Man page
normalize,MSnSet-method Man page
normalize,OnDiskMSnExp-method Man page
normalize,Spectrum2-method Man page
normalize,Spectrum-method Man page
notes<-,MIAPE-method Man page
notes,MIAPE-method Man page
notes,pSet-method Man page
npcv Man page
nQuants Man page
nrow,MSmap-method Man page
objlog Man page
OnDiskMSnExp Man page
[,OnDiskMSnExp,ANY,ANY,ANY-method Man page
[[,OnDiskMSnExp,ANY,ANY-method Man page
[[,OnDiskMSnExp,ANY,ANY,missing-method Man page
[[,OnDiskMSnExp,ANY,missing,missing-method Man page
OnDiskMSnExp-class Man page
[,OnDiskMSnExp,logicalOrNumeric,missing,missing-method Man page
[[,OnDiskMSnExp-method Man page
otherInfo,MIAPE-method Man page
pData,pSet-method Man page
peaksCount Man page
peaksCount,OnDiskMSnExp,missing-method Man page
peaksCount,OnDiskMSnExp,numeric-method Man page
peaksCount,pSet,missing-method Man page
peaksCount,pSet,numeric-method Man page
peaksCount,Spectrum,missing-method Man page
peptides,MzTab-method Man page
phenoData,pSet-method Man page
pickPeaks Man page
pickPeaks-methods Man page
pickPeaks,MSnExp-method Man page
pickPeaks,MSnExp-method Man page
pickPeaks,OnDiskMSnExp-method Man page
pickPeaks,Spectrum-method Man page
pickPeaks,Spectrum-method Man page
plot Man page
plot2d Man page
plot2d,data.frame-method Man page
plot2d-methods Man page
plot2d,MSnExp-method Man page
plot3D Man page
plot3D,MSmap-method Man page
plotDensity Man page
plotDensity,data.frame-method Man page
plotDensity-methods Man page
plotDensity,MSnExp-method Man page
plot-methods Man page
plot,MSmap,missing-method Man page
plot,MSnExp Man page
plot.MSnExp Man page
plot,MSnExp,missing-method Man page
plotMzDelta Man page
plotMzDelta-methods Man page
plotMzDelta,MSnExp-method Man page
plotMzDelta,mzRramp-method Man page
plotNA Man page
plotNA,matrix-method Man page
plotNA-methods Man page
plotNA,MSnSet-method Man page
plot.Spectrum Man page
plot,Spectrum2,character-method Man page
plot.Spectrum.character Man page
plot,Spectrum-method Man page
plot,Spectrum,missing-method Man page
plot.Spectrum.Spectrum Man page
plot,Spectrum,Spectrum-method Man page
polarity Man page
polarity,OnDiskMSnExp-method Man page
polarity,pSet-method Man page
polarity,Spectrum-method Man page
precAcquisitionNum Man page
precAcquisitionNum,pSet-method Man page
precAcquisitionNum,Spectrum-method Man page
precScanNum Man page
precScanNum,OnDiskMSnExp-method Man page
precScanNum,OnDiskMSnExp-method Man page
precScanNum,pSet-method Man page
precScanNum,Spectrum-method Man page
precSelection Man page
precSelectionTable Man page
precursorCharge Man page
precursorCharge,OnDiskMSnExp-method Man page
precursorCharge,pSet-method Man page
precursorCharge,Spectrum-method Man page
precursorIntensity Man page
precursorIntensity,OnDiskMSnExp-method Man page
precursorIntensity,pSet-method Man page
precursorIntensity,Spectrum-method Man page
precursorMz Man page
precursorMz,OnDiskMSnExp-method Man page
precursorMz,pSet-method Man page
precursorMz,Spectrum-method Man page
processingData Man page
processingData,MSnSet-method Man page
processingData,pSet-method Man page
ProcessingStep Man page
ProcessingStep-class Man page
ProcessingStep:OnDiskMSnExp Man page
proteins,MzTab-method Man page
protocolData,pSet-method Man page
pSet Man page
[,pSet,ANY,ANY,ANY-method Man page
[,pSet,ANY,ANY-method Man page
[[,pSet,ANY,ANY-method Man page
pSet-class Man page
[,pSet-method Man page
[[,pSet-method Man page
psms,MzTab-method Man page
pubMedIds<-,MIAPE-method Man page
pubMedIds,MIAPE-method Man page
pubMedIds,pSet-method Man page
purityCorrect Man page
purityCorrect-methods Man page
purityCorrect,MSnSet,matrix-method Man page
purityCorrect,MSnSet-method Man page
qual Man page
qual,MSnSet-method Man page
quantify Man page
quantify-methods 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
ratios,MSnSet-method Man page
readMgfData Man page
readMSData Man page
readMSData2 Man page
readMSnSet Man page
readMSnSet2 Man page
readMzTabData Man page
readMzTabData_v0.9 Man page
readMzXMLData Man page
removeMultipleAssignment Man page
removeMultipleAssignment-method Man page
removeMultipleAssignment,MSnExp-method Man page
removeMultipleAssignment,MSnSet-method Man page
removeNoId Man page
removeNoId-methods Man page
removeNoId,MSnExp-method Man page
removeNoId,MSnSet-method Man page
removePeaks Man page
removePeaks-methods Man page
removePeaks,MSnExp-method Man page
removePeaks,MSnExp-method Man page
removePeaks,OnDiskMSnExp-method Man page
removePeaks,Spectrum-method Man page
removePeaks,Spectrum-method Man page
removeReporters Man page
removeReporters-methods Man page
removeReporters,MSnExp-method Man page
removeReporters,OnDiskMSnExp-method Man page
removeReporters,Spectrum-method Man page
reporterColors Man page
reporterColors-method Man page
reporterColors,ReporterIons-method Man page
reporterColours Man page
reporterColours-method Man page
reporterColours,ReporterIons-method Man page
ReporterIons Man page
[,ReporterIons,ANY,ANY,ANY-method Man page
[,ReporterIons,ANY,ANY-method Man page
ReporterIons-class Man page
[,ReporterIons-method Man page
reporterNames Man page
reporterNames<- Man page
reporterNames-method Man page
reporterNames<-,ReporterIons,ANY-method Man page
reporterNames<-,ReporterIons,character-method Man page
reporterNames<-,ReporterIons-method Man page
reporterNames,ReporterIons-method Man page
rmFeaturesOfInterest Man page
rmFeaturesOfInterest,FoICollection,numeric-method Man page
rmFeaturesOfInterest-methods Man page
rtime Man page
rtime,MSmap-method Man page
rtime,OnDiskMSnExp-method Man page
rtime,pSet-method Man page
rtime,Spectrum-method Man page
sampleNames<-,pSet,character-method Man page
sampleNames,pSet-method Man page
samples,MIAPE-method Man page
scale,MSnSet-method Man page
scanIndex Man page
scanIndex,OnDiskMSnExp-method Man page
scanIndex,pSet-method Man page
scanIndex,Spectrum-method Man page
selectFeatureData Man page
setMSnbaseParallelThresh Man page
setMSnbaseVerbose Man page
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,MSnSetList-method Man page
show,MSnSet-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
smallMolecules Man page
smooth Man page
smoothed Man page
smoothed<- Man page
smoothed<-,OnDiskMSnExp,logical-method Man page
smoothed,OnDiskMSnExp-method Man page
smoothed<-,pSet,ANY-method Man page
smoothed<-,pSet,logical-method Man page
smoothed,pSet-method Man page
smoothed<-,Spectrum,ANY-method Man page
smoothed<-,Spectrum,logical-method Man page
smoothed,Spectrum-method Man page
smooth-methods Man page
smooth,MSnExp-method Man page
smooth,MSnExp-method Man page
smooth,OnDiskMSnExp-method Man page
smooth,Spectrum-method Man page
smooth,Spectrum-method Man page
spectra Man page
spectra,MSnExp-method Man page
spectra,OnDiskMSnExp-method Man page
spectra,pSet-method Man page
Spectrum Man page
Spectrum1 Man page
Spectrum1-class Man page
Spectrum2 Man page
Spectrum2-class Man page
Spectrum-class Man page
split,MSnSet,character-method Man page
split,MSnSet,factor-method Man page
tic Man page
tic,OnDiskMSnExp-method Man page
tic,pSet-method Man page
tic,Spectrum-method Man page
t,MSmap-method Man page
t.MSnSet Man page
TMT10 Man page
TMT10ETD Man page
TMT10HCD Man page
TMT6 Man page
TMT6b Man page
TMT7 Man page
TMT7b Man page
topN Man page
topN,matrix-method Man page
topN,MSnSet-method Man page
topN,MSnSet,MSnSet-method Man page
trimMz Man page
trimMz-methods Man page
trimMz,MSnExp-method Man page
trimMz,MSnExp-method Man page
trimMz,MSnExp,numeric-method Man page
trimMz,OnDiskMSnExp,numeric-method Man page
trimMz,Spectrum-method Man page
trimMz,Spectrum-method Man page
trimMz,Spectrum,numeric-method Man page
trimws Man page
trimws,data.frame-method Man page
trimws,MSnSet-method Man page
unique1 Man page
unique1,FeatComp-method Man page
unique1,methods Man page
unique2 Man page
unique2,FeatComp-method Man page
unique2,methods Man page
unsplit,MSnSetList,factor-method Man page
updateFeatureNames Man page
updateFvarLabels Man page
updateObject,MSnExp-method Man page
updateObject,Spectrum-method Man page
updateSampleNames Man page
validateOnDiskMSnExp Man page
varLabels,pSet-method Man page
varMetadata,pSet-method Man page
whichNA Man page
width Man page
width-method Man page
width,ReporterIons-method Man page
write.exprs Man page
write.exprs,MSnSet-method Man page
writeMgfData Man page
writeMgfData-methods Man page
writeMgfData,MSnExp-method Man page
writeMgfData,Spectrum-method Man page
writeMzTabData Man page
xic Man page
xic,character-method Man page
xic-methods Man page
xic,mzRramp-method Man page

Files

MSnbase/.Rinstignore
MSnbase/CONDUCT.md
MSnbase/DESCRIPTION
MSnbase/NAMESPACE
MSnbase/NEWS
MSnbase/R
MSnbase/R/AllClassUnions.R MSnbase/R/AllGenerics.R MSnbase/R/DataClasses.R MSnbase/R/MzTab.R MSnbase/R/RcppExports.R MSnbase/R/TMT10.R MSnbase/R/TMT6.R MSnbase/R/TMT7.R MSnbase/R/averageMSnSet.R MSnbase/R/cache.R MSnbase/R/combineFeatures.R MSnbase/R/compfnames.R MSnbase/R/environment.R MSnbase/R/foi.R MSnbase/R/functions-MIAPE.R MSnbase/R/functions-MSnExp.R MSnbase/R/functions-MSnProcess.R MSnbase/R/functions-MSnSet.R MSnbase/R/functions-OnDiskMSnExp.R MSnbase/R/functions-ReporterIons.R MSnbase/R/functions-Spectrum.R MSnbase/R/functions-Spectrum1.R MSnbase/R/functions-Spectrum2.R MSnbase/R/functions-fragments.R MSnbase/R/functions-mzR.R MSnbase/R/header.R MSnbase/R/hmap.R MSnbase/R/iPQF.R MSnbase/R/iTRAQ4.R MSnbase/R/iTRAQ5.R MSnbase/R/iTRAQ8.R MSnbase/R/iTRAQ9.R MSnbase/R/imputation.R MSnbase/R/map.R MSnbase/R/matching.R MSnbase/R/methods-MIAPE.R MSnbase/R/methods-MSnExp.R MSnbase/R/methods-MSnProcess.R MSnbase/R/methods-MSnSet.R MSnbase/R/methods-MSnSetList.R MSnbase/R/methods-NAnnotatedDataFrame.R MSnbase/R/methods-OnDiskMSnExp.R MSnbase/R/methods-ProcessingStep.R MSnbase/R/methods-ReporterIons.R MSnbase/R/methods-Spectrum.R MSnbase/R/methods-Spectrum1.R MSnbase/R/methods-Spectrum2.R MSnbase/R/methods-all.equal.R MSnbase/R/methods-filters.R MSnbase/R/methods-fragments.R MSnbase/R/methods-mzR.R MSnbase/R/methods-other.R MSnbase/R/methods-pSet.R MSnbase/R/methods-updateObjectTo.R MSnbase/R/missing-data.R MSnbase/R/nadata.R MSnbase/R/options.R MSnbase/R/plotting-MSnExp.R MSnbase/R/plotting-MSnSet.R MSnbase/R/plotting-OnDiskMSnExp.R MSnbase/R/plotting-Spectrum.R MSnbase/R/plotting-Spectrum1.R MSnbase/R/plotting-Spectrum2.R MSnbase/R/plotting-dataframe.R MSnbase/R/quantitation-MS2-isobaric.R MSnbase/R/quantitation-MS2-labelfree.R MSnbase/R/readMSData.R MSnbase/R/readMSData2.R MSnbase/R/readMSnSet.R MSnbase/R/readMzXMLData.R MSnbase/R/readWriteMgfData.R MSnbase/R/readWriteMzTab.R MSnbase/R/utils.R MSnbase/R/zzz.R
MSnbase/README.Rmd
MSnbase/README.md
MSnbase/build
MSnbase/build/vignette.rds
MSnbase/data
MSnbase/data/TMT10.RData
MSnbase/data/TMT10ETD.RData
MSnbase/data/TMT10HCD.RData
MSnbase/data/TMT6.RData
MSnbase/data/TMT6b.RData
MSnbase/data/TMT7.RData
MSnbase/data/TMT7b.RData
MSnbase/data/iTRAQ4.RData
MSnbase/data/iTRAQ5.RData
MSnbase/data/iTRAQ8.RData
MSnbase/data/iTRAQ9.RData
MSnbase/data/itraqdata.RData
MSnbase/data/msnset.rda
MSnbase/data/msnset2.rda
MSnbase/data/naset.rda
MSnbase/inst
MSnbase/inst/CITATION
MSnbase/inst/doc
MSnbase/inst/doc/MSnbase-demo
MSnbase/inst/doc/MSnbase-demo.R
MSnbase/inst/doc/MSnbase-demo.Rnw
MSnbase/inst/doc/MSnbase-demo.pdf
MSnbase/inst/doc/MSnbase-development
MSnbase/inst/doc/MSnbase-development.R
MSnbase/inst/doc/MSnbase-development.Rnw
MSnbase/inst/doc/MSnbase-development.pdf
MSnbase/inst/doc/MSnbase-io
MSnbase/inst/doc/MSnbase-io.R
MSnbase/inst/doc/MSnbase-io.Rnw
MSnbase/inst/doc/MSnbase-io.pdf
MSnbase/inst/doc/benchmarking.R
MSnbase/inst/doc/benchmarking.Rmd
MSnbase/inst/doc/benchmarking.html
MSnbase/inst/extdata
MSnbase/inst/extdata/M.rda
MSnbase/inst/extdata/M2.rda
MSnbase/inst/extdata/TMT6plexPurityCorrections.csv
MSnbase/inst/extdata/dummyiTRAQ.mzXML
MSnbase/inst/extdata/dummyiTRAQ.mzid
MSnbase/inst/extdata/iTRAQ4plexPurityCorrections.csv
MSnbase/inst/extdata/iTRAQ8plexPurityCorrections.csv
MSnbase/inst/extdata/ipqfres.rda
MSnbase/inst/extdata/msx.rda
MSnbase/inst/extdata/msx0.rda
MSnbase/inst/extdata/test.mgf
MSnbase/inst/scripts
MSnbase/inst/scripts/benchmarking.R
MSnbase/inst/scripts/make_msx.R
MSnbase/inst/scripts/naset.R
MSnbase/inst/scripts/torture.R
MSnbase/inst/tests
MSnbase/man
MSnbase/man/FeatComp-class.Rd MSnbase/man/FeaturesOfInterest-class.Rd MSnbase/man/MIAPE-class.Rd MSnbase/man/MSmap-class.Rd MSnbase/man/MSnExp-class.Rd MSnbase/man/MSnProcess-class.Rd MSnbase/man/MSnSet-class.Rd MSnbase/man/MSnSetList-class.Rd MSnbase/man/MSnbase-package.Rd MSnbase/man/MSnbaseOptions.Rd MSnbase/man/MzTab-class.Rd MSnbase/man/NAnnotatedDataFrame-class.Rd MSnbase/man/OnDiskMSnExp-class.Rd MSnbase/man/ProcessingStep-class.Rd MSnbase/man/ReporterIons-class.Rd MSnbase/man/Spectrum-class.Rd MSnbase/man/Spectrum1-class.Rd MSnbase/man/Spectrum2-class.Rd MSnbase/man/TMT6.Rd MSnbase/man/addIdentificationData-methods.Rd MSnbase/man/averageMSnSet.Rd MSnbase/man/bin-methods.Rd MSnbase/man/calculateFragments-methods.Rd MSnbase/man/chromatogram-methods.Rd MSnbase/man/clean-methods.Rd MSnbase/man/combineFeatures.Rd MSnbase/man/commonFeatureNames.Rd MSnbase/man/compareMSnSets.Rd MSnbase/man/compareSpectra-methods.Rd MSnbase/man/defunct.Rd MSnbase/man/estimateNoise-method.Rd MSnbase/man/exprsToRatios-methods.Rd MSnbase/man/extractPrecSpectra-methods.Rd MSnbase/man/featureCV.Rd MSnbase/man/fillUp.Rd MSnbase/man/formatRt.Rd MSnbase/man/get.amino.acids.Rd MSnbase/man/get.atomic.mass.Rd MSnbase/man/getVariableName.Rd MSnbase/man/grepEcols.Rd MSnbase/man/iPQF.Rd MSnbase/man/iTRAQ4.Rd MSnbase/man/imageNA2.Rd MSnbase/man/impute-methods.Rd MSnbase/man/itraqdata.Rd MSnbase/man/listOf.Rd MSnbase/man/makeNaData.Rd MSnbase/man/missing-data.Rd MSnbase/man/nQuants.Rd MSnbase/man/naplot.Rd MSnbase/man/normalise-methods.Rd MSnbase/man/npcv.Rd MSnbase/man/pSet-class.Rd MSnbase/man/pickPeaks-method.Rd MSnbase/man/plot-methods.Rd MSnbase/man/plot2d-methods.Rd MSnbase/man/plotDensity-methods.Rd MSnbase/man/plotMzDelta-methods.Rd MSnbase/man/plotNA-methods.Rd MSnbase/man/plotSpectrumSpectrum-methods.Rd MSnbase/man/precSelection.Rd MSnbase/man/purityCorrect-methods.Rd MSnbase/man/quantify-methods.Rd MSnbase/man/readMSData.Rd MSnbase/man/readMSnSet.Rd MSnbase/man/readMgfData.Rd MSnbase/man/readMzTabData.Rd MSnbase/man/readMzTabData_v0.9.Rd MSnbase/man/removeNoId-methods.Rd MSnbase/man/removePeaks-methods.Rd MSnbase/man/removeReporters-methods.Rd MSnbase/man/selectFeatureData.Rd MSnbase/man/smooth-methods.Rd MSnbase/man/trimMz-methods.Rd MSnbase/man/updateObject-methods.Rd MSnbase/man/writeMgfData-methods.Rd MSnbase/man/xic-methods.Rd
MSnbase/src
MSnbase/src/MSnbase.h
MSnbase/src/RcppExports.cpp
MSnbase/src/Spectrum1_class.c
MSnbase/src/Spectrum2_class.c
MSnbase/src/imp_neighbour_avg.cpp
MSnbase/src/utils.c
MSnbase/tests
MSnbase/tests/testthat
MSnbase/tests/testthat.R
MSnbase/tests/testthat/dont_test_plotMzDelata.R
MSnbase/tests/testthat/test_MIAPE.R
MSnbase/tests/testthat/test_MSmap.R
MSnbase/tests/testthat/test_MSnExp.R
MSnbase/tests/testthat/test_MSnExpFilters.R
MSnbase/tests/testthat/test_MSnExpSubsetting.R
MSnbase/tests/testthat/test_MSnProcess.R
MSnbase/tests/testthat/test_MSnSet.R
MSnbase/tests/testthat/test_MzTab.R
MSnbase/tests/testthat/test_MzTab_09.R
MSnbase/tests/testthat/test_NAnnotatedDataFrame.R
MSnbase/tests/testthat/test_OnDiskMSnExp.R
MSnbase/tests/testthat/test_OnDiskMSnExp2.R
MSnbase/tests/testthat/test_OnDiskMSnExp_other_methods.R
MSnbase/tests/testthat/test_ProcessingStep.R
MSnbase/tests/testthat/test_ReportersIons.R
MSnbase/tests/testthat/test_Spectrum.R
MSnbase/tests/testthat/test_Spectrum_Constructor.R
MSnbase/tests/testthat/test_average.R
MSnbase/tests/testthat/test_cache.R
MSnbase/tests/testthat/test_centroided.R
MSnbase/tests/testthat/test_compfnames.R
MSnbase/tests/testthat/test_defunct.R
MSnbase/tests/testthat/test_equalMSnExps.R
MSnbase/tests/testthat/test_fileNames.R
MSnbase/tests/testthat/test_filterNA.R
MSnbase/tests/testthat/test_foi.R
MSnbase/tests/testthat/test_fragments.R
MSnbase/tests/testthat/test_iPQF.R
MSnbase/tests/testthat/test_impute.R
MSnbase/tests/testthat/test_io.R
MSnbase/tests/testthat/test_matching.R
MSnbase/tests/testthat/test_mzR-funs.R
MSnbase/tests/testthat/test_nadata.R
MSnbase/tests/testthat/test_plotting.R
MSnbase/tests/testthat/test_purity.R
MSnbase/tests/testthat/test_quant.R
MSnbase/tests/testthat/test_readMSData2.R
MSnbase/tests/testthat/test_readWriteMgfData.R
MSnbase/tests/testthat/test_topN.R
MSnbase/tests/testthat/test_trimws.R
MSnbase/tests/testthat/test_updateObjects.R
MSnbase/tests/testthat/test_utils.R
MSnbase/vignettes
MSnbase/vignettes/Bugs.tex
MSnbase/vignettes/Foreword.tex
MSnbase/vignettes/MSnbase-demo.Rnw
MSnbase/vignettes/MSnbase-development.Rnw
MSnbase/vignettes/MSnbase-io.Rnw
MSnbase/vignettes/MSnbase.bib
MSnbase/vignettes/NOTES.org
MSnbase/vignettes/NoteAboutSpeedAndMemory.tex
MSnbase/vignettes/benchmarking.Rmd
MSnbase/vignettes/itraqchem.pdf
MSnbase/vignettes/msnset.png
MSnbase/vignettes/plot2d-figure.png
MSnbase/vignettes/plotDensity-figure.png
MSnbase/vignettes/plotMzDelta-pride12011.pdf
MSnbase/vignettes/tmt10comp.pdf

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

Please suggest features or report bugs with the GitHub issue tracker.

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