Base Functions and Classes for Mass Spectrometry and Proteomics

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Documentation for package ‘MSnbase’ version 2.33.4

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

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A B C D E F G H I L M N O P Q R S T U V W misc

-- A --

abstract-method	The "MIAPE" Class for Storing Proteomics Experiment Information
abstract-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
acquisitionNum	The "Spectrum" Class
acquisitionNum-method	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
acquisitionNum-method	List of Spectrum objects along with annotations
acquisitionNum-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
acquisitionNum-method	The "Spectrum" Class
acquisitionNum-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
addFeaturesOfInterest	Features of Interest
addFeaturesOfInterest-method	Features of Interest
addFeaturesOfInterest-methods	Features of Interest
addIdentificationData	Adds Identification Data
addIdentificationData-method	The 'MSnExp' Class for MS Data And Meta-Data
addIdentificationData-method	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
addIdentificationData-methods	Adds Identification Data
addMSnSetMetadata	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
aggregationFun	Representation of chromatographic MS data
aggvar	Identify aggregation outliers
alignRt-method	Representation of chromatographic MS data
alignRt-method	Container for multiple Chromatogram objects
all.equal-method	The 'MSnExp' Class for MS Data And Meta-Data
analyser	The "MIAPE" Class for Storing Proteomics Experiment Information
analyser-method	The "MIAPE" Class for Storing Proteomics Experiment Information
analyser-method	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
analyser-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
analyserDetails	The "MIAPE" Class for Storing Proteomics Experiment Information
analyserDetails-method	The "MIAPE" Class for Storing Proteomics Experiment Information
analyserDetails-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
analyzer	The "MIAPE" Class for Storing Proteomics Experiment Information
analyzer-method	The "MIAPE" Class for Storing Proteomics Experiment Information
analyzer-method	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
analyzer-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
analyzerDetails	The "MIAPE" Class for Storing Proteomics Experiment Information
analyzerDetails-method	The "MIAPE" Class for Storing Proteomics Experiment Information
analyzerDetails-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
as	Coerce identification data to a 'data.frame'
as.data.frame-method	Representation of chromatographic MS data
as.data.frame.MSnExp	The 'MSnExp' Class for MS Data And Meta-Data
as.data.frame.MSnSet	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
as.data.frame.mzRident	Coerce identification data to a 'data.frame'
as.data.frame.Spectrum	The "Spectrum" Class
as.ExpressionSet.MSnSet	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
as.matrix.FoICollection	Features of Interest
as.MIAME.MIAPE	The "MIAPE" Class for Storing Proteomics Experiment Information
as.MSnExp.OnDiskMSnExp	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
as.MSnSet.ExpressionSet	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
assayData-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
assayData-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
averageMSnSet	Generate an average 'MSnSet'

-- B --

bin	Bin 'MSnExp' or 'Spectrum' instances
bin-method	Representation of chromatographic MS data
bin-method	Container for multiple Chromatogram objects
bin-method	The 'MSnExp' Class for MS Data And Meta-Data
bin-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
bin-method	The "Spectrum" Class
bin-methods	Bin 'MSnExp' or 'Spectrum' instances
bpi	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
bpi-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data

-- C --

c-method	Container for multiple Chromatogram objects
calculateFragments	Calculate ions produced by fragmentation.
calculateFragments-method	The "Spectrum2" Class for MSn Spectra
calculateFragments-method	Calculate ions produced by fragmentation.
centroided	The "Spectrum" Class
centroided-method	List of Spectrum objects along with annotations
centroided-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
centroided-method	The "Spectrum" Class
centroided-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
centroided<-	The "Spectrum" Class
centroided<--method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
centroided<--method	The "Spectrum" Class
centroided<--method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
Chromatogram	Representation of chromatographic MS data
chromatogram	Extract chromatogram object(s)
Chromatogram-class	Representation of chromatographic MS data
chromatogram-method	Extract chromatogram object(s)
class:MIAPE	The "MIAPE" Class for Storing Proteomics Experiment Information
class:MSnExp	The 'MSnExp' Class for MS Data And Meta-Data
class:MSnProcess	The "MSnProcess" Class
class:MSnSet	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
class:MzTab	Parse 'MzTab' files
class:OnDiskMSnExp	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
class:pSet	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
class:ReporterIons	The "ReporterIons" Class
class:Spectrum	The "Spectrum" Class
class:Spectrum1	The "Spectrum1" Class for MS1 Spectra
class:Spectrum2	The "Spectrum2" Class for MSn Spectra
clean	Clean 'MSnExp', 'Spectrum' or 'Chromatogram' instances
clean-method	Representation of chromatographic MS data
clean-method	Container for multiple Chromatogram objects
clean-method	The 'MSnExp' Class for MS Data And Meta-Data
clean-method	List of Spectrum objects along with annotations
clean-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
clean-method	The "Spectrum" Class
clean-methods	Clean 'MSnExp', 'Spectrum' or 'Chromatogram' instances
coerce-method	Features of Interest
coerce-method	Container for multiple Chromatogram objects
coerce-method	The "MIAPE" Class for Storing Proteomics Experiment Information
coerce-method	Class 'MSmap'
coerce-method	The 'MSnExp' Class for MS Data And Meta-Data
coerce-method	The "MSnProcess" Class
coerce-method	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
coerce-method	List of Spectrum objects along with annotations
coerce-method	Parse 'MzTab' files
coerce-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
coerce-method	The "Spectrum" Class
coerce-method	Conversion between objects from the Spectra and MSnbase packages
coerce-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
coerce-method	Import peptide-spectrum matches
collisionEnergy	The "Spectrum2" Class for MSn Spectra
collisionEnergy-method	List of Spectrum objects along with annotations
collisionEnergy-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
collisionEnergy-method	The "Spectrum2" Class for MSn Spectra
collisionEnergy-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
colnames<--method	Container for multiple Chromatogram objects
combine-method	The "MIAPE" Class for Storing Proteomics Experiment Information
combine-method	The "MSnProcess" Class
combine-method	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
combineFeatures	Combines features in an 'MSnSet' object
combineFeatures-method	Combines features in an 'MSnSet' object
combineSpectra	Combine Spectra
combineSpectra-method	Combine Spectra
combineSpectraMovingWindow	Combine signal from consecutive spectra of LCMS experiments
comments	Parse 'MzTab' files
common	Class '"FeatComp"'
common,methods	Class '"FeatComp"'
common-method	Class '"FeatComp"'
commonFeatureNames	Keep only common feature names
compareChromatograms	Representation of chromatographic MS data
compareChromatograms-method	Representation of chromatographic MS data
compareChromatograms-method	Container for multiple Chromatogram objects
compareMSnSets	Compare two MSnSets
compareSpectra	Compare Spectra of an 'MSnExp' or 'Spectrum' instances
compareSpectra-method	The 'MSnExp' Class for MS Data And Meta-Data
compareSpectra-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
compareSpectra-method	The "Spectrum" Class
compareSpectra-methods	Compare Spectra of an 'MSnExp' or 'Spectrum' instances
compfnames	Class '"FeatComp"'
compfnames-method	Class '"FeatComp"'
compfnames-methods	Class '"FeatComp"'
consensusSpectrum	Combine spectra to a consensus spectrum

-- D --

description-method	Features of Interest
description-method	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
description-method	The "ReporterIons" Class
description-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
detectorType	The "MIAPE" Class for Storing Proteomics Experiment Information
detectorType-method	The "MIAPE" Class for Storing Proteomics Experiment Information
detectorType-method	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
detectorType-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
dim	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
dim-method	Class 'MSmap'
dim-method	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
dim-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
droplevels.MSnSet	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data

-- E --

estimateMzResolution	Estimate the m/z resolution of a spectrum
estimateMzResolution-method	Estimate the m/z resolution of a spectrum
estimateMzScattering	Estimate m/z scattering in consecutive scans
estimateNoise	Noise Estimation for 'Spectrum' instances
estimateNoise-method	The 'MSnExp' Class for MS Data And Meta-Data
estimateNoise-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
estimateNoise-method	The "Spectrum" Class
estimateNoise-methods	Noise Estimation for 'Spectrum' instances
executeProcessingStep	Simple processing step class
expandFeatureVars	Expand or merge feature variables
expemail	The "MIAPE" Class for Storing Proteomics Experiment Information
expemail-method	The "MIAPE" Class for Storing Proteomics Experiment Information
expemail-method	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
expemail-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
experimentData-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
experimentData<--method	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
expinfo-method	The "MIAPE" Class for Storing Proteomics Experiment Information
exprs-method	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
exptitle	The "MIAPE" Class for Storing Proteomics Experiment Information
exptitle-method	The "MIAPE" Class for Storing Proteomics Experiment Information
exptitle-method	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
exptitle-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
extractPrecSpectra	Extracts precursor-specific spectra from an 'MSnExp' object
extractPrecSpectra-method	The 'MSnExp' Class for MS Data And Meta-Data
extractPrecSpectra-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
extractPrecSpectra-methods	Extracts precursor-specific spectra from an 'MSnExp' object
extractSpectraData	Conversion between objects from the Spectra and MSnbase packages

-- F --

factorsAsStrings	Converts factors to strings
fData-method	Container for multiple Chromatogram objects
fData-method	Storing multiple related MSnSets
fData-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
fData<--method	Container for multiple Chromatogram objects
fData<--method	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
fData<--method	Storing multiple related MSnSets
fData<--method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
FeatComp-class	Class '"FeatComp"'
featureCV	Calculates coeffivient of variation for features
featureData-method	Container for multiple Chromatogram objects
featureData-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
featureData<--method	Container for multiple Chromatogram objects
featureNames-method	Container for multiple Chromatogram objects
featureNames-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
featureNames-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
featureNames<--method	Container for multiple Chromatogram objects
featureNames<--method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
FeaturesOfInterest	Features of Interest
FeaturesOfInterest-class	Features of Interest
FeaturesOfInterest-method	Features of Interest
FeaturesOfInterest-methods	Features of Interest
fileName-method	Class 'MSmap'
fileName-method	Parse 'MzTab' files
fileNames	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
fileNames-method	Class 'MSmap'
fileNames-method	The "MSnProcess" Class
fileNames-method	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
fileNames-method	Parse 'MzTab' files
fileNames-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
fillUp	Fills up a vector
filterAcquisitionNum	The 'MSnExp' Class for MS Data And Meta-Data
filterAcquisitionNum-method	The 'MSnExp' Class for MS Data And Meta-Data
filterEmptySpectra	The 'MSnExp' Class for MS Data And Meta-Data
filterEmptySpectra-method	The 'MSnExp' Class for MS Data And Meta-Data
filterFile	The 'MSnExp' Class for MS Data And Meta-Data
filterFile-method	The 'MSnExp' Class for MS Data And Meta-Data
filterIdentificationDataFrame	Filter out unreliable PSMs.
filterIntensity-method	Representation of chromatographic MS data
filterIntensity-method	Container for multiple Chromatogram objects
filterIsolationWindow	The 'MSnExp' Class for MS Data And Meta-Data
filterIsolationWindow-method	The 'MSnExp' Class for MS Data And Meta-Data
filterMsLevel	The 'MSnExp' Class for MS Data And Meta-Data
filterMsLevel-method	The 'MSnExp' Class for MS Data And Meta-Data
filterMsLevel-method	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
filterMsLevel-method	List of Spectrum objects along with annotations
filterMz	Trims 'MSnExp' or 'Spectrum' instances
filterMz-method	The 'MSnExp' Class for MS Data And Meta-Data
filterMz-method	List of Spectrum objects along with annotations
filterMz-method	The "Spectrum" Class
filtermz-method	The "Spectrum" Class
filterMz-methods	Trims 'MSnExp' or 'Spectrum' instances
filterNA	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
filterNA-method	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
filterPolarity	The 'MSnExp' Class for MS Data And Meta-Data
filterPolarity-method	The 'MSnExp' Class for MS Data And Meta-Data
filterPrecursorMz	The 'MSnExp' Class for MS Data And Meta-Data
filterPrecursorMz-method	The 'MSnExp' Class for MS Data And Meta-Data
filterPrecursorScan	The 'MSnExp' Class for MS Data And Meta-Data
filterPrecursorScan-method	The 'MSnExp' Class for MS Data And Meta-Data
filterRt	The 'MSnExp' Class for MS Data And Meta-Data
filterRt-method	Representation of chromatographic MS data
filterRt-method	The 'MSnExp' Class for MS Data And Meta-Data
filterZero	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
filterZero-method	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
fnamesIn	Features of Interest
fnamesIn-method	Features of Interest
fnamesIn-methods	Features of Interest
foi	Features of Interest
foi-method	Features of Interest
foi-methods	Features of Interest
FoICollection	Features of Interest
FoICollection-class	Features of Interest
FoICollection-method	Features of Interest
FoICollection-methods	Features of Interest
formatRt	Format Retention Time
fromFile	The "Spectrum" Class
fromFile-method	Representation of chromatographic MS data
fromFile-method	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
fromFile-method	List of Spectrum objects along with annotations
fromFile-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
fromFile-method	The "Spectrum" Class
fromFile-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
fvarLabels-method	Container for multiple Chromatogram objects
fvarLabels-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
fvarMetadata-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata

-- G --

getEcols	Returns the matching column names of indices.
getVariableName	Return a variable name
grepEcols	Returns the matching column names of indices.

-- H --

hasChromatograms	Checks if raw data files have any spectra or chromatograms
hasSpectra	Checks if raw data files have any spectra or chromatograms
header	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
header-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
header-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata

-- I --

idSummary	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
idSummary-method	The 'MSnExp' Class for MS Data And Meta-Data
idSummary-method	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
image-method	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
image2	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
imageNA2	NA heatmap visualisation for 2 groups
impute-method	Quantitative proteomics data imputation
instrumentCustomisations	The "MIAPE" Class for Storing Proteomics Experiment Information
instrumentCustomisations-method	The "MIAPE" Class for Storing Proteomics Experiment Information
instrumentCustomisations-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
instrumentManufacturer	The "MIAPE" Class for Storing Proteomics Experiment Information
instrumentManufacturer-method	The "MIAPE" Class for Storing Proteomics Experiment Information
instrumentManufacturer-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
instrumentModel	The "MIAPE" Class for Storing Proteomics Experiment Information
instrumentModel-method	The "MIAPE" Class for Storing Proteomics Experiment Information
instrumentModel-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
intensity	The "Spectrum" Class
intensity-method	Representation of chromatographic MS data
intensity-method	List of Spectrum objects along with annotations
intensity-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
intensity-method	The "Spectrum" Class
intensity-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
ionCount	The "Spectrum" Class
ionCount-method	List of Spectrum objects along with annotations
ionCount-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
ionCount-method	The "Spectrum" Class
ionCount-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
ionSource	The "MIAPE" Class for Storing Proteomics Experiment Information
ionSource-method	The "MIAPE" Class for Storing Proteomics Experiment Information
ionSource-method	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
ionSource-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
ionSourceDetails	The "MIAPE" Class for Storing Proteomics Experiment Information
ionSourceDetails-method	The "MIAPE" Class for Storing Proteomics Experiment Information
ionSourceDetails-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
iPQF	iPQF: iTRAQ (and TMT) Protein Quantification based on Features
is.na.MSnSet	Exploring missing data in 'MSnSet' instances
isCentroided	The "Spectrum" Class
isCentroided-method	The 'MSnExp' Class for MS Data And Meta-Data
isCentroided-method	List of Spectrum objects along with annotations
isCentroided-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
isCentroided-method	The "Spectrum" Class
isCentroidedFromFile	Get mode from mzML data file
isEmpty-method	Representation of chromatographic MS data
isEmpty-method	Container for multiple Chromatogram objects
isEmpty-method	List of Spectrum objects along with annotations
isEmpty-method	The "Spectrum" Class
isMSnbaseFastLoad	MSnbase options
isMSnbaseVerbose	MSnbase options
isolationWindow-method	The 'MSnExp' Class for MS Data And Meta-Data
isolationWindowLowerMz	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
isolationWindowLowerMz-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
isolationWindowLowerMz-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
isolationWindowUpperMz	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
isolationWindowUpperMz-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
isolationWindowUpperMz-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
iTRAQ4	iTRAQ 4-plex set
iTRAQ5	iTRAQ 4-plex set
iTRAQ8	iTRAQ 4-plex set
iTRAQ9	iTRAQ 4-plex set
itraqdata	Example 'MSnExp' and 'MSnSet' data sets

-- L --

lapply-method	Storing multiple related MSnSets
length	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
length-method	Representation of chromatographic MS data
length-method	Features of Interest
length-method	Storing multiple related MSnSets
length-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
length-method	The "ReporterIons" Class
length-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
lengths-method	Features of Interest
listOf	Tests equality of list elements class
log-method	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data

-- M --

makeCamelCase	Convert to camel case by replacing dots by captial letters
makeImpuritiesMatrix	Performs reporter ions purity correction
makeNaData	Create a data with missing values
makeNaData2	Create a data with missing values
MAplot-method	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
MChromatograms	Container for multiple Chromatogram objects
MChromatograms-class	Container for multiple Chromatogram objects
meanMzInts	Combine a list of spectra to a single spectrum
meanSdPlot-method	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
mergeFeatureVars	Expand or merge feature variables
metadata-method	Parse 'MzTab' files
MIAPE	The "MIAPE" Class for Storing Proteomics Experiment Information
MIAPE-class	The "MIAPE" Class for Storing Proteomics Experiment Information
missing-data	Documenting missing data visualisation
missingdata	Documenting missing data visualisation
moleculeEvidence	Parse 'MzTab' files
moleculeFeatures	Parse 'MzTab' files
ms2df	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
msInfo	The "MIAPE" Class for Storing Proteomics Experiment Information
msInfo-method	The "MIAPE" Class for Storing Proteomics Experiment Information
msInfo-method	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
msInfo-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
msLevel	The "Spectrum" Class
msLevel-method	Representation of chromatographic MS data
msLevel-method	Class 'MSmap'
msLevel-method	List of Spectrum objects along with annotations
msLevel-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
msLevel-method	The "Spectrum" Class
msLevel-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
MSmap	Class 'MSmap'
msMap	Class 'MSmap'
MSmap-class	Class 'MSmap'
MSmap-method	Class 'MSmap'
msMap-method	Class 'MSmap'
MSnbaseOptions	MSnbase options
MSnExp	The 'MSnExp' Class for MS Data And Meta-Data
MSnExp-class	The 'MSnExp' Class for MS Data And Meta-Data
MSnProcess	The "MSnProcess" Class
MSnProcess-class	The "MSnProcess" Class
MSnSet	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
msnset	Example 'MSnExp' and 'MSnSet' data sets
MSnSet-class	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
msnset2	Example 'MSnExp' and 'MSnSet' data sets
MSnSetList	Storing multiple related MSnSets
MSnSetList-class	Storing multiple related MSnSets
msnsets	Storing multiple related MSnSets
MSpectra	List of Spectrum objects along with annotations
MSpectra-class	List of Spectrum objects along with annotations
mz	The "Spectrum" Class
mz-method	Representation of chromatographic MS data
mz-method	Container for multiple Chromatogram objects
mz-method	Class 'MSmap'
mz-method	List of Spectrum objects along with annotations
mz-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
mz-method	The "ReporterIons" Class
mz-method	The "Spectrum" Class
mz-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
mzRes	Class 'MSmap'
mzRes-method	Class 'MSmap'
MzTab	Parse 'MzTab' files
MzTab-class	Parse 'MzTab' files
mzTabMode	Parse 'MzTab' files
mzTabType	Parse 'MzTab' files

-- N --

names-method	Class '"FeatComp"'
names-method	Features of Interest
names-method	Storing multiple related MSnSets
names-method	The "ReporterIons" Class
names<--method	Features of Interest
names<--method	Storing multiple related MSnSets
naplot	Overview of missing value
naset	Quantitative proteomics data imputation
ncol-method	Class 'MSmap'
nFeatures	How many features in a group?
normalise	Normalisation of 'MSnExp', 'MSnSet' and 'Spectrum' objects
normalise-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
normalise-method	Normalisation of 'MSnExp', 'MSnSet' and 'Spectrum' objects
normalise-methods	Normalisation of 'MSnExp', 'MSnSet' and 'Spectrum' objects
normalize	Normalisation of 'MSnExp', 'MSnSet' and 'Spectrum' objects
normalize-method	Representation of chromatographic MS data
normalize-method	Container for multiple Chromatogram objects
normalize-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
normalize-method	Normalisation of 'MSnExp', 'MSnSet' and 'Spectrum' objects
normalize-methods	Normalisation of 'MSnExp', 'MSnSet' and 'Spectrum' objects
normToReference	Combine peptides into proteins.
notes-method	The "MIAPE" Class for Storing Proteomics Experiment Information
notes-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
notes<--method	The "MIAPE" Class for Storing Proteomics Experiment Information
npcv	Non-parametric coefficient of variation
nQuants	Count the number of quantitfied features.
nrow-method	Class 'MSmap'
NTR	Combine peptides into proteins.

-- O --

objlog	Storing multiple related MSnSets
OnDiskMSnExp	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
OnDiskMSnExp-class	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
otherInfo-method	The "MIAPE" Class for Storing Proteomics Experiment Information

-- P --

pData-method	Container for multiple Chromatogram objects
pData-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
pData<--method	Container for multiple Chromatogram objects
pData<--method	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
pData<--method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
peaksCount	The "Spectrum" Class
peaksCount-method	List of Spectrum objects along with annotations
peaksCount-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
peaksCount-method	The "Spectrum" Class
peaksCount-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
peptides-method	Parse 'MzTab' files
phenoData-method	Container for multiple Chromatogram objects
phenoData-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
phenoData<--method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
pickPeaks	Peak Detection for 'MSnExp' or 'Spectrum' instances
pickPeaks-method	The 'MSnExp' Class for MS Data And Meta-Data
pickPeaks-method	List of Spectrum objects along with annotations
pickPeaks-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
pickPeaks-method	The "Spectrum" Class
pickPeaks-methods	Peak Detection for 'MSnExp' or 'Spectrum' instances
plot	Plotting 'MSnExp' and 'Spectrum' object(s)
plot,MSnExp	The 'MSnExp' Class for MS Data And Meta-Data
plot-method	Representation of chromatographic MS data
plot-method	Container for multiple Chromatogram objects
plot-method	Class 'MSmap'
plot-method	The 'MSnExp' Class for MS Data And Meta-Data
plot-method	Plotting 'MSnExp' and 'Spectrum' object(s)
plot-method	Plotting a 'Spectrum' vs another 'Spectrum' object.
plot-methods	Plotting 'MSnExp' and 'Spectrum' object(s)
plot.MSnExp	Plotting 'MSnExp' and 'Spectrum' object(s)
plot.Spectrum	Plotting 'MSnExp' and 'Spectrum' object(s)
plot.Spectrum.character	Plotting 'MSnExp' and 'Spectrum' object(s)
plot.Spectrum.Spectrum	Plotting a 'Spectrum' vs another 'Spectrum' object.
plot2d	The 'plot2d' method for 'MSnExp' quality assessment
plot2d-method	The 'plot2d' method for 'MSnExp' quality assessment
plot2d-methods	The 'plot2d' method for 'MSnExp' quality assessment
plot3D	Class 'MSmap'
plot3D-method	Class 'MSmap'
plotDensity	The 'plotDensity' method for 'MSnExp' quality assessment
plotDensity-method	The 'plotDensity' method for 'MSnExp' quality assessment
plotDensity-methods	The 'plotDensity' method for 'MSnExp' quality assessment
plotMzDelta	The delta m/z plot
plotMzDelta-method	The delta m/z plot
plotMzDelta-methods	The delta m/z plot
plotNA	Exploring missing data in 'MSnSet' instances
plotNA-method	Exploring missing data in 'MSnSet' instances
plotNA-methods	Exploring missing data in 'MSnSet' instances
polarity	The "Spectrum" Class
polarity-method	Container for multiple Chromatogram objects
polarity-method	List of Spectrum objects along with annotations
polarity-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
polarity-method	The "Spectrum" Class
polarity-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
precAcquisitionNum	The "Spectrum2" Class for MSn Spectra
precAcquisitionNum-method	The "Spectrum2" Class for MSn Spectra
precAcquisitionNum-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
precScanNum	The "Spectrum2" Class for MSn Spectra
precScanNum-method	List of Spectrum objects along with annotations
precScanNum-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
precScanNum-method	The "Spectrum2" Class for MSn Spectra
precScanNum-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
precSelection	Number of precursor selection events
precSelectionTable	Number of precursor selection events
precursorCharge	The "Spectrum2" Class for MSn Spectra
precursorCharge-method	List of Spectrum objects along with annotations
precursorCharge-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
precursorCharge-method	The "Spectrum2" Class for MSn Spectra
precursorCharge-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
precursorIntensity	The "Spectrum2" Class for MSn Spectra
precursorIntensity-method	List of Spectrum objects along with annotations
precursorIntensity-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
precursorIntensity-method	The "Spectrum2" Class for MSn Spectra
precursorIntensity-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
precursorMz	The "Spectrum2" Class for MSn Spectra
precursorMz-method	Representation of chromatographic MS data
precursorMz-method	Container for multiple Chromatogram objects
precursorMz-method	List of Spectrum objects along with annotations
precursorMz-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
precursorMz-method	The "Spectrum2" Class for MSn Spectra
precursorMz-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
processingData	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
processingData-method	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
processingData-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
ProcessingStep	Simple processing step class
ProcessingStep-class	Simple processing step class
ProcessingStep:OnDiskMSnExp	Simple processing step class
productMz-method	Representation of chromatographic MS data
productMz-method	Container for multiple Chromatogram objects
proteins-method	Parse 'MzTab' files
protocolData-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
pSet	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
pSet-class	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
psms-method	Parse 'MzTab' files
pubMedIds-method	The "MIAPE" Class for Storing Proteomics Experiment Information
pubMedIds-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
pubMedIds<--method	The "MIAPE" Class for Storing Proteomics Experiment Information
purityCorrect	Performs reporter ions purity correction
purityCorrect-method	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
purityCorrect-methods	Performs reporter ions purity correction

-- Q --

qual	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
qual-method	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
quantify	Quantifies 'MSnExp' and 'Spectrum' objects
quantify-method	The 'MSnExp' Class for MS Data And Meta-Data
quantify-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
quantify-method	The "Spectrum" Class
quantify-methods	Quantifies 'MSnExp' and 'Spectrum' objects

-- R --

readMgfData	Import mgf files as 'MSnExp' instances.
readMSData	Imports mass-spectrometry raw data files as 'MSnExp' instances.
readMSData2	Imports mass-spectrometry raw data files as 'MSnExp' instances.
readMSnSet	Read 'MSnSet'
readMSnSet2	Read 'MSnSet'
readMzIdData	Import peptide-spectrum matches
readMzTabData	Read an 'mzTab' file
readMzTabData_v0.9	Read an 'mzTab' file
readSRMData	Read SRM/MRM chromatographic data
reduce-method	Reduce a data.frame
removeMultipleAssignment	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
removeMultipleAssignment-method	The 'MSnExp' Class for MS Data And Meta-Data
removeMultipleAssignment-method	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
removeNoId	Removes non-identified features
removeNoId-method	The 'MSnExp' Class for MS Data And Meta-Data
removeNoId-method	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
removeNoId-methods	Removes non-identified features
removePeaks	Removes low intensity peaks
removePeaks-method	The 'MSnExp' Class for MS Data And Meta-Data
removePeaks-method	List of Spectrum objects along with annotations
removePeaks-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
removePeaks-method	The "Spectrum" Class
removePeaks-methods	Removes low intensity peaks
removeReporters	Removes reporter ion tag peaks
removeReporters-method	The 'MSnExp' Class for MS Data And Meta-Data
removeReporters-method	The "Spectrum2" Class for MSn Spectra
removeReporters-methods	Removes reporter ion tag peaks
reporterColors	The "ReporterIons" Class
reporterColors-method	The "ReporterIons" Class
reporterColours	The "ReporterIons" Class
reporterColours-method	The "ReporterIons" Class
ReporterIons	The "ReporterIons" Class
ReporterIons-class	The "ReporterIons" Class
reporterNames	The "ReporterIons" Class
reporterNames-method	The "ReporterIons" Class
reporterNames<-	The "ReporterIons" Class
reporterNames<--method	The "ReporterIons" Class
requiredFvarLabels	Select feature variables of interest
rmFeaturesOfInterest	Features of Interest
rmFeaturesOfInterest-method	Features of Interest
rmFeaturesOfInterest-methods	Features of Interest
rownames<--method	Container for multiple Chromatogram objects
rtime	The "Spectrum" Class
rtime-method	Representation of chromatographic MS data
rtime-method	Class 'MSmap'
rtime-method	List of Spectrum objects along with annotations
rtime-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
rtime-method	The "Spectrum" Class
rtime-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata

-- S --

sampleNames-method	Container for multiple Chromatogram objects
sampleNames-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
sampleNames<--method	Container for multiple Chromatogram objects
sampleNames<--method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
samples-method	The "MIAPE" Class for Storing Proteomics Experiment Information
sapply-method	Storing multiple related MSnSets
scale-method	Normalisation of 'MSnExp', 'MSnSet' and 'Spectrum' objects
scanIndex	The "Spectrum" Class
scanIndex-method	List of Spectrum objects along with annotations
scanIndex-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
scanIndex-method	The "Spectrum" Class
scanIndex-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
selectFeatureData	Select feature variables of interest
setMSnbaseFastLoad	MSnbase options
setMSnbaseParallelThresh	MSnbase options
setMSnbaseVerbose	MSnbase options
show-method	Representation of chromatographic MS data
show-method	Class '"FeatComp"'
show-method	Features of Interest
show-method	Container for multiple Chromatogram objects
show-method	The "MIAPE" Class for Storing Proteomics Experiment Information
show-method	Class 'MSmap'
show-method	The 'MSnExp' Class for MS Data And Meta-Data
show-method	The "MSnProcess" Class
show-method	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
show-method	Storing multiple related MSnSets
show-method	List of Spectrum objects along with annotations
show-method	Parse 'MzTab' files
show-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
show-method	Simple processing step class
show-method	The "ReporterIons" Class
show-method	The "Spectrum" Class
smallMolecules	Parse 'MzTab' files
smooth	Smooths 'MSnExp' or 'Spectrum' instances
smooth-method	The 'MSnExp' Class for MS Data And Meta-Data
smooth-method	List of Spectrum objects along with annotations
smooth-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
smooth-method	The "Spectrum" Class
smooth-methods	Smooths 'MSnExp' or 'Spectrum' instances
smoothed	The "Spectrum" Class
smoothed-method	List of Spectrum objects along with annotations
smoothed-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
smoothed-method	The "Spectrum" Class
smoothed-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
smoothed<-	The "Spectrum" Class
smoothed<--method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
smoothed<--method	The "Spectrum" Class
smoothed<--method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
spectra	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
spectra-method	The 'MSnExp' Class for MS Data And Meta-Data
spectra-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
spectra-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
spectrapply	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
spectrapply-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
spectrapply-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
Spectrum	The "Spectrum" Class
Spectrum-class	The "Spectrum" Class
Spectrum1	The "Spectrum1" Class for MS1 Spectra
Spectrum1-class	The "Spectrum1" Class for MS1 Spectra
Spectrum2	The "Spectrum2" Class for MSn Spectra
Spectrum2-class	The "Spectrum2" Class for MSn Spectra
split-method	Storing multiple related MSnSets
splitByFile	The 'MSnExp' Class for MS Data And Meta-Data
splitByFile-method	The 'MSnExp' Class for MS Data And Meta-Data

-- T --

t-method	Class 'MSmap'
t.MSnSet	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
tic	The "Spectrum" Class
tic-method	List of Spectrum objects along with annotations
tic-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
tic-method	The "Spectrum" Class
tic-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
TMT10	TMT 6/10-plex sets
TMT10ETD	TMT 6/10-plex sets
TMT10HCD	TMT 6/10-plex sets
TMT11	TMT 6/10-plex sets
TMT11HCD	TMT 6/10-plex sets
TMT16	TMT 6/10-plex sets
TMT16HCD	TMT 6/10-plex sets
TMT6	TMT 6/10-plex sets
TMT6b	TMT 6/10-plex sets
TMT7	TMT 6/10-plex sets
TMT7b	TMT 6/10-plex sets
topN	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
topN-method	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
transformIntensity	Representation of chromatographic MS data
transformIntensity-method	Representation of chromatographic MS data
transformIntensity-method	Container for multiple Chromatogram objects
trimMz	Trims 'MSnExp' or 'Spectrum' instances
trimMz-method	The 'MSnExp' Class for MS Data And Meta-Data
trimMz-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
trimMz-method	The "Spectrum" Class
trimMz-methods	Trims 'MSnExp' or 'Spectrum' instances
trimws	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
trimws-method	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data

-- U --

unique1	Class '"FeatComp"'
unique1,methods	Class '"FeatComp"'
unique1-method	Class '"FeatComp"'
unique2	Class '"FeatComp"'
unique2,methods	Class '"FeatComp"'
unique2-method	Class '"FeatComp"'
unsplit-method	Storing multiple related MSnSets
updateFeatureNames	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
updateFvarLabels	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
updateObject-method	Update MSnbase objects
updateSampleNames	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data

-- V --

validateOnDiskMSnExp	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
varLabels-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
varMetadata-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata

-- W --

whichNA	Create a data with missing values
width	The "ReporterIons" Class
width-method	The "ReporterIons" Class
write.exprs	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
write.exprs-method	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
writeMgfData	Write an experiment or spectrum to an mgf file
writeMgfData-method	List of Spectrum objects along with annotations
writeMgfData-method	Write an experiment or spectrum to an mgf file
writeMgfData-methods	Write an experiment or spectrum to an mgf file
writeMSData	Write MS data to mzML or mzXML files
writeMSData-method	Write MS data to mzML or mzXML files
writeMzTabData	Export an MzTab object as mzTab file.

-- misc --

$-method	Container for multiple Chromatogram objects
$-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
$<--method	Container for multiple Chromatogram objects
$<--method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
[-method	Features of Interest
[-method	Container for multiple Chromatogram objects
[-method	The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
[-method	Storing multiple related MSnSets
[-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
[-method	The "ReporterIons" Class
[-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
[<--method	Container for multiple Chromatogram objects
[[-method	Features of Interest
[[-method	Storing multiple related MSnSets
[[-method	The 'OnDiskMSnExp' Class for MS Data And Meta-Data
[[-method	Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata