# Base Functions and Classes for Mass Spectrometry and Proteomics

## Documentation for package ‘MSnbase’ version 2.34.1

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

## Help Pages

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