All functions

Chromatogram() aggregationFun() show(<Chromatogram>) rtime(<Chromatogram>) intensity(<Chromatogram>) mz(<Chromatogram>) precursorMz(<Chromatogram>) fromFile(<Chromatogram>) length(<Chromatogram>) as.data.frame(<Chromatogram>) filterRt(<Chromatogram>) clean(<Chromatogram>) plot(<Chromatogram>,<ANY>) msLevel(<Chromatogram>) isEmpty(<Chromatogram>) productMz(<Chromatogram>) bin(<Chromatogram>)

Representation of chromatographic MS data

FeatComp-class

Class "FeatComp"

FeaturesOfInterest-class

Features of Interest

MChromatograms() show(<MChromatograms>) `[`(<MChromatograms>,<ANY>,<ANY>,<ANY>) `[<-`(<MChromatograms>) plot(<MChromatograms>,<ANY>) phenoData(<MChromatograms>) pData(<MChromatograms>) `pData<-`(<MChromatograms>,<data.frame>) `$`(<MChromatograms>) `$<-`(<MChromatograms>) `colnames<-`(<MChromatograms>) sampleNames(<MChromatograms>) `sampleNames<-`(<MChromatograms>,<ANY>) isEmpty(<MChromatograms>) featureNames(<MChromatograms>) `featureNames<-`(<MChromatograms>) featureData(<MChromatograms>) `featureData<-`(<MChromatograms>,<ANY>) fData(<MChromatograms>) `fData<-`(<MChromatograms>,<ANY>) fvarLabels(<MChromatograms>) `rownames<-`(<MChromatograms>) precursorMz(<MChromatograms>) productMz(<MChromatograms>) mz(<MChromatograms>) polarity(<MChromatograms>) bin(<MChromatograms>) clean(<MChromatograms>)

Container for multiple Chromatogram objects

MIAPE-class

The "MIAPE" Class for Storing Proteomics Experiment Information

MSmap-class

Class MSmap

MSnExp-class

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

MSnProcess-class

The "MSnProcess" Class

MSnSet-class

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

MSnSetList-class

Storing multiple related MSnSets

MSnbaseOptions() isMSnbaseVerbose() setMSnbaseVerbose() setMSnbaseParallelThresh() setMSnbaseFastLoad() isMSnbaseFastLoad()

MSnbase options

MSpectra() mz(<MSpectra>) intensity(<MSpectra>) rtime(<MSpectra>) precursorMz(<MSpectra>) precursorCharge(<MSpectra>) precScanNum(<MSpectra>) precursorIntensity(<MSpectra>) acquisitionNum(<MSpectra>) scanIndex(<MSpectra>) peaksCount(<MSpectra>,<ANY>) msLevel(<MSpectra>) tic(<MSpectra>) ionCount(<MSpectra>) collisionEnergy(<MSpectra>) fromFile(<MSpectra>) polarity(<MSpectra>) smoothed(<MSpectra>) isEmpty(<MSpectra>) centroided(<MSpectra>) isCentroided(<MSpectra>) writeMgfData(<MSpectra>) clean(<MSpectra>) removePeaks(<MSpectra>) filterMz(<MSpectra>) pickPeaks(<MSpectra>) smooth(<MSpectra>) filterMsLevel(<MSpectra>)

List of Spectrum objects along with annotations

MzTab-class

Parse MzTab files

OnDiskMSnExp-class

The OnDiskMSnExp Class for MS Data And Meta-Data

ProcessingStep-class

Simple processing step class

ReporterIons-class

The "ReporterIons" Class

Spectrum-class

The "Spectrum" Class

Spectrum1-class

The "Spectrum1" Class for MS1 Spectra

Spectrum2-class

The "Spectrum2" Class for MSn Spectra

TMT6 TMT6b TMT7 TMT7b TMT10 TMT10ETD TMT10HCD TMT11 TMT11HCD

TMT 6/10-plex sets

addIdentificationData-methods

Adds Identification Data

aggvar()

Identify aggregation outliers

averageMSnSet()

Generate an average MSnSet

bin-methods

Bin 'MSnExp' or 'Spectrum' instances

calculateFragments-methods

Calculate ions produced by fragmentation.

chromatogram(<MSnExp>)

Extract chromatogram object(s)

clean-methods

Clean 'MSnExp', 'Spectrum' or 'Chromatogram' instances

combineFeatures

Combines features in an MSnSet object

combineSpectra(<MSnExp>) combineSpectra(<MSpectra>)

Combine Spectra

combineSpectraMovingWindow()

Combine signal from consecutive spectra of LCMS experiments

commonFeatureNames()

Keep only common feature names

compareMSnSets()

Compare two MSnSets

compareSpectra-methods

Compare Spectra of an 'MSnExp' or 'Spectrum' instances

consensusSpectrum()

Combine spectra to a consensus spectrum

estimateMzResolution(<MSnExp>) estimateMzResolution(<Spectrum>)

Estimate the m/z resolution of a spectrum

estimateMzScattering()

Estimate m/z scattering in consecutive scans

estimateNoise-methods

Noise Estimation for 'Spectrum' instances

extractPrecSpectra-methods

Extracts precursor-specific spectra from an 'MSnExp' object

extractSpectraData()

Extract data from MSnbase objects for use in Spectra

expandFeatureVars() mergeFeatureVars()

Expand or merge feature variables

factorsAsStrings()

Converts factors to strings

featureCV()

Calculates coeffivient of variation for features

fillUp()

Fills up a vector

filterIdentificationDataFrame()

Filter out unreliable PSMs.

formatRt()

Format Retention Time

get.amino.acids()

Amino acids

get.atomic.mass()

Atomic mass.

getVariableName()

Return a variable name

grepEcols() getEcols()

Returns the matching column names of indices.

hasSpectra() hasChromatograms()

Checks if raw data files have any spectra or chromatograms

iPQF()

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

iTRAQ4 iTRAQ5 iTRAQ8 iTRAQ9

iTRAQ 4-plex set

imageNA2()

NA heatmap visualisation for 2 groups

impute-methods

Quantitative proteomics data imputation

isCentroidedFromFile()

Get mode from mzML data file

itraqdata

Example MSnExp and MSnSet data sets

listOf()

Tests equality of list elements class

makeCamelCase()

Convert to camel case by replacing dots by captial letters

makeNaData() makeNaData2() whichNA()

Create a data with missing values

meanMzInts()

Combine a list of spectra to a single spectrum

missing-data

Documenting missing data visualisation

as

Coerce identification data to a data.frame

nFeatures()

How many features in a group?

nQuants()

Count the number of quantitfied features.

naplot()

Overview of missing value

navMS() nextMS() prevMS()

Navigate an MSnExp object

normToReference()

Combine peptides into proteins.

normalise-methods

Normalisation of MSnExp, MSnSet and Spectrum objects

npcv()

Non-parametric coefficient of variation

pSet-class

Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata

pickPeaks-methods

Peak Detection for 'MSnExp' or 'Spectrum' instances

plot-methods

Plotting 'MSnExp' and 'Spectrum' object(s)

plot2d-methods

The 'plot2d' method for 'MSnExp' quality assessment

plotDensity-methods

The 'plotDensity' method for 'MSnExp' quality assessment

plotMzDelta-methods

The delta m/z plot

plotNA-methods

Exploring missing data in 'MSnSet' instances

plot.Spectrum.Spectrum-methods

Plotting a 'Spectrum' vs another 'Spectrum' object.

precSelection()

Number of precursor selection events

purityCorrect-methods

Performs reporter ions purity correction

quantify-methods

Quantifies 'MSnExp' and 'Spectrum' objects

readMSData()

Imports mass-spectrometry raw data files as 'MSnExp' instances.

readMSnSet() readMSnSet2()

Read 'MSnSet'

readMgfData()

Import mgf files as 'MSnExp' instances.

readMzIdData()

Import peptide-spectrum matches

readMzTabData()

Read an 'mzTab' file

readMzTabData_v0.9()

Read an 'mzTab' file

readSRMData()

Read SRM/MRM chromatographic data

reduce(<data.frame>)

Reduce a data.frame

removeNoId-methods

Removes non-identified features

removePeaks-methods

Removes low intensity peaks

removeReporters-methods

Removes reporter ion tag peaks

selectFeatureData() requiredFvarLabels()

Select feature variables of interest

smooth-methods

Smooths 'MSnExp' or 'Spectrum' instances

trimMz-methods

Trims 'MSnExp' or 'Spectrum' instances

updateObject-methods

Update MSnbase objects

writeMSData(<MSnExp>,<character>)

Write MS data to mzML or mzXML files

writeMgfData-methods

Write an experiment or spectrum to an mgf file

writeMzTabData()

Export an MzTab object as mzTab file.