Base Functions and Classes for Mass Spectrometry and Proteomics

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Documentation for package ‘MSnbase’ version 2.4.0

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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 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
aggregationFun Representation of chromatographic MS data
aggvar Identify aggregation outliers
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.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 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 --

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 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)
Chromatograms Container for multiple Chromatogram objects
Chromatograms-class Container for multiple Chromatogram objects
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:NAnnotatedDataFrame Class Containing Measured Variables and Their Meta-Data Description for Multiplexed Experiments.
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 The 'MSnExp' Class for MS Data And Meta-Data
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 The "MIAPE" Class for Storing Proteomics Experiment Information
coerce-method Class 'MSmap'
coerce-method The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
coerce-method Parse 'MzTab' files
coerce-method The 'OnDiskMSnExp' Class for MS Data And Meta-Data
coerce-method The "Spectrum" Class
coerce-method Import peptide-spectrum matches
collisionEnergy The "Spectrum2" Class for MSn Spectra
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
comments Parse 'MzTab' files
common Class '"FeatComp"'
common,methods Class '"FeatComp"'
common-method Class '"FeatComp"'
commonFeatureNames Keep only common feature names
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"'

-- D --

defaultNeutralLoss Calculate ions produced by fragmentation.
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 Containing Measured Variables and Their Meta-Data Description for Multiplexed Experiments.
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 --

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
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
exprsToRatios Calculate all ratio pairs
exprsToRatios-method Calculate all ratio pairs
exprsToRatios-methods Calculate all ratio pairs
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

-- F --

factorsAsStrings Converts factors to strings
fData-method Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
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 Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
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 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.
filterMsLevel The 'MSnExp' Class for MS Data And Meta-Data
filterMsLevel-method The 'MSnExp' Class for MS Data And Meta-Data
filterMz Trims 'MSnExp' or 'Spectrum' instances
filterMz-method The 'MSnExp' Class for MS Data And Meta-Data
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
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 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 Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
fvarMetadata-method Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata

-- G --

get.amino.acids Amino acids
get.atomic.mass Atomic mass.
getEcols Returns the matching column names of indices.
getRatios Calculate all ratio pairs
getVariableName Return a variable name
grepEcols Returns the matching column names of indices.

-- H --

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 Quantitative proteomics data imputation
impute-method Quantitative proteomics data imputation
impute-methods Quantitative proteomics data imputation
imputeMethods 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 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 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 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 The "Spectrum" Class
isMSnbaseFastLoad MSnbase options
isMSnbaseVerbose MSnbase options
isolationWindow-method The 'MSnExp' Class for MS Data And Meta-Data
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
meanSdPlot-method The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
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
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 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'
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
multiLabels Class Containing Measured Variables and Their Meta-Data Description for Multiplexed Experiments.
multiLabels-method Class Containing Measured Variables and Their Meta-Data Description for Multiplexed Experiments.
multiplex Class Containing Measured Variables and Their Meta-Data Description for Multiplexed Experiments.
multiplex-method Class Containing Measured Variables and Their Meta-Data Description for Multiplexed Experiments.
mz The "Spectrum" Class
mz-method Representation of chromatographic MS data
mz-method Class 'MSmap'
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
NAnnotatedDataFrame Class Containing Measured Variables and Their Meta-Data Description for Multiplexed Experiments.
NAnnotatedDataFrame-class Class Containing Measured Variables and Their Meta-Data Description for Multiplexed Experiments.
naplot Overview of missing value
naset Quantitative proteomics data imputation
navMS Navigate an 'MSnExp' object
ncol-method Class 'MSmap'
nextMS Navigate an 'MSnExp' object
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 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 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
pickPeaks Peak Detection for 'MSnExp' or 'Spectrum' instances
pickPeaks-method The 'MSnExp' Class for MS Data And Meta-Data
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 '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 'Spectrum' object(s)
plot-method Plotting a 'Spectrum' vs another 'Spectrum' object.
plot-methods Plotting 'Spectrum' object(s)
plot.MSnExp Plotting 'Spectrum' object(s)
plot.Spectrum Plotting 'Spectrum' object(s)
plot.Spectrum.character Plotting '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 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 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 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 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 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
prevMS Navigate an 'MSnExp' object
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 Representation of chromatographic MS data
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
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 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
rmFeaturesOfInterest Features of Interest
rmFeaturesOfInterest-method Features of Interest
rmFeaturesOfInterest-methods Features of Interest
rtime The "Spectrum" Class
rtime-method Representation of chromatographic MS data
rtime-method Class 'MSmap'
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
scale-method Normalisation of 'MSnExp', 'MSnSet' and 'Spectrum' objects
scanIndex The "Spectrum" Class
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 Container for multiple Chromatogram objects
show-method Class '"FeatComp"'
show-method Features of Interest
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 Parse 'MzTab' files
show-method Class Containing Measured Variables and Their Meta-Data Description for Multiplexed Experiments.
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 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 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 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
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
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 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

-- 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 Container for multiple Chromatogram objects
[-method Features of Interest
[-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