MSnbase: Base Functions and Classes for MS-based Proteomics

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Documentation for package ‘MSnbase’ version 1.8.0

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

-- 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 "Spectrum" Class
acquisitionNum-method Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
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.data.frame.Spectrum The "Spectrum" Class
as.ExpressionSet.MSnSet The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
assayData-method Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata

-- C --

centroided The "Spectrum" Class
centroided-method The "Spectrum" Class
centroided-method Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
centroided<- The "Spectrum" Class
centroided<--method The "Spectrum" Class
centroided<--method Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
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:NAnnotatedDataFrame Class Containing Measured Variables and Their Meta-Data Description for Multiplexed Experiments.
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 MSMS Spectra
clean Cleans 'MSnExp' or 'Spectrum' instances
clean-method The 'MSnExp' Class for MS Data And Meta-Data
clean-method The "Spectrum" Class
clean-methods Cleans 'MSnExp' or 'Spectrum' instances
coerce-method The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
coerce-method The "Spectrum" Class
collisionEnergy The "Spectrum2" Class for MSMS Spectra
collisionEnergy-method The "Spectrum2" Class for MSMS Spectra
collisionEnergy-method Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
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

-- D --

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 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 --

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

-- F --

fData-method Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
featureCV Calculates coeffivient of variation for features
featureData-method Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
featureNames-method Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
fileNames Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
fileNames-method The "MSnProcess" Class
fileNames-method The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
fileNames-method Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
fillUp Fills up a vector
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
formatRt Format Retention Time
fromFile The "Spectrum" Class
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 --

getRatios Calculate all ratio pairs
getVariableName Return a variable name

-- H --

header Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
header-method Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata

-- I --

image-method The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
impute Quantitative proteomics data imputation
impute-method Quantitative proteomics data imputation
impute-methods 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 The "Spectrum" Class
intensity-method Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
ionCount The "Spectrum" Class
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
is.na.MSnSet Exploring missing data in 'MSnSet' instances
iTRAQ4 iTRAQ 4-plex set
iTRAQ5 iTRAQ 4-plex set
iTRAQ8 iTRAQ 4-plex set
iTRAQ9 iTRAQ 4-plex set
itraqdata Example 'MSnExp' data set

-- L --

length Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
length-method The "ReporterIons" Class
length-method Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
log-method The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data

-- M --

makeImpuritiesMatrix Performs reporter ions purity correction
makeMTD Creates the mzTab metadata section
makePEP Creates the mzTab peptide section
makePRT Creates the mzTab protein section
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
MIAPE The "MIAPE" Class for Storing Proteomics Experiment Information
MIAPE-class The "MIAPE" Class for Storing Proteomics Experiment Information
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 The "Spectrum" Class
msLevel-method Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
MSnbase MSnbase: Base Functions and Classes for MS-based Proteomics
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-class The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
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 The "ReporterIons" Class
mz-method The "Spectrum" Class
mz-method Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata

-- N --

names-method The "ReporterIons" Class
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.
normalise Normalisation of 'MSnExp', 'MSnSet' and 'Spectrum' objects
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 Normalisation of 'MSnExp', 'MSnSet' and 'Spectrum' objects
normalize-methods Normalisation of 'MSnExp', 'MSnSet' and 'Spectrum' objects
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
nQuants Count the number of quantitfied features.

-- O --

otherInfo-method The "MIAPE" Class for Storing Proteomics Experiment Information

-- P --

pData-method Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
peaksCount The "Spectrum" Class
peaksCount-method The "Spectrum" Class
peaksCount-method Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
phenoData-method Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
plot Plotting 'Spectrum' object(s)
plot,MSnExp The 'MSnExp' Class for MS Data And Meta-Data
plot-method The 'MSnExp' Class for MS Data And Meta-Data
plot-method The "Spectrum" Class
plot-methods Plotting 'Spectrum' object(s)
plot.MSnExp Plotting 'Spectrum' object(s)
plot.Spectrum Plotting 'Spectrum' object(s)
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
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 for 'MSnExp' quality assessment
plotMzDelta-method The delta m/z plot for 'MSnExp' quality assessment
plotMzDelta-methods The delta m/z plot for 'MSnExp' quality assessment
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 "Spectrum1" Class for MS1 Spectra
polarity-method The "Spectrum1" Class for MS1 Spectra
polarity-method Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
precAcquisitionNum The "Spectrum2" Class for MSMS Spectra
precAcquisitionNum-method The "Spectrum2" Class for MSMS Spectra
precAcquisitionNum-method Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
precScanNum The "Spectrum2" Class for MSMS Spectra
precScanNum-method The "Spectrum2" Class for MSMS 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 MSMS Spectra
precursorCharge-method The "Spectrum2" Class for MSMS Spectra
precursorCharge-method Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
precursorIntensity The "Spectrum2" Class for MSMS Spectra
precursorIntensity-method The "Spectrum2" Class for MSMS Spectra
precursorIntensity-method Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
precursorMz The "Spectrum2" Class for MSMS Spectra
precursorMz-method The "Spectrum2" Class for MSMS 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
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
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 "Spectrum" Class
quantify-methods Quantifies 'MSnExp' and 'Spectrum' objects

-- R --

readIspyData Reads an ispy2 result spread sheet and creates a fully featured 'MSnSet' instance.
readMgfData Import mgf files as 'MSnExp' instances.
readMSData Imports mass-spectrometry raw data files as 'MSnExp' instances.
readMSnSet Read 'MSnSet'
readMzTabData Read an 'mzTab' file
removePeaks Removes low intensity peaks
removePeaks-method The 'MSnExp' 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 MSMS 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
rtime The "Spectrum" Class
rtime-method The "Spectrum" Class
rtime-method Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata

-- S --

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 "Spectrum" Class
scanIndex-method Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
show-method The "MIAPE" Class for Storing Proteomics Experiment Information
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 Class Containing Measured Variables and Their Meta-Data Description for Multiplexed Experiments.
show-method The "ReporterIons" Class
show-method The "Spectrum" Class
spectra Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
spectra-method The 'MSnExp' Class for MS Data And Meta-Data
spectra-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 MSMS Spectra
Spectrum2-class The "Spectrum2" Class for MSMS Spectra

-- T --

t.MSnSet The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
tic The "Spectrum" Class
tic-method The "Spectrum" Class
tic-method Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
TMT6 TMT 6-plex set
TMT7 TMT 6-plex set
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 "Spectrum" Class
trimMz-methods Trims 'MSnExp' or 'Spectrum' instances

-- U --

updateFeatureNames The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
updateFvarLabels The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
updateSampleNames The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data

-- V --

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 --

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
writeMzTabData Writes an 'MSnSet' to an mzTab file

-- misc --

[-method The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
[-method The "ReporterIons" Class
[-method Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
[[-method Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata