Man pages for MSnbase
Base Functions and Classes for Mass Spectrometry and Proteomics

addIdentificationData-methodsAdds Identification Data
aggvarIdentify aggregation outliers
averageMSnSetGenerate an average 'MSnSet'
bin-methodsBin 'MSnExp' or 'Spectrum' instances
calculateFragments-methodsCalculate ions produced by fragmentation.
Chromatogram-classRepresentation of chromatographic MS data
chromatogram-MSnExp-methodExtract chromatogram object(s)
clean-methodsClean 'MSnExp', 'Spectrum' or 'Chromatogram' instances
combineFeaturesCombines features in an 'MSnSet' object
combineSpectraCombine Spectra
combineSpectraMovingWindowCombine signal from consecutive spectra of LCMS experiments
commonFeatureNamesKeep only common feature names
compareMSnSetsCompare two MSnSets
compareSpectra-methodsCompare Spectra of an 'MSnExp' or 'Spectrum' instances
consensusSpectrumCombine spectra to a consensus spectrum
defunctMSnbase Deprecated and Defunct
estimateMzResolutionEstimate the m/z resolution of a spectrum
estimateMzScatteringEstimate m/z scattering in consecutive scans
estimateNoise-methodNoise Estimation for 'Spectrum' instances
extractPrecSpectra-methodsExtracts precursor-specific spectra from an 'MSnExp' object
extractSpectraDataExtract data from MSnbase objects for use in Spectra
factorsAsStringsConverts factors to strings
fData-utilsExpand or merge feature variables
FeatComp-classClass '"FeatComp"'
featureCVCalculates coeffivient of variation for features
FeaturesOfInterest-classFeatures of Interest
fillUpFills up a vector
filterIdentificationDataFrameFilter out unreliable PSMs.
formatRtFormat Retention Time
get.amino.acidsAmino acids
get.atomic.massAtomic mass.
getVariableNameReturn a variable name
grepEcolsReturns the matching column names of indices.
hasSpectraOrChromatogramsChecks if raw data files have any spectra or chromatograms
imageNA2NA heatmap visualisation for 2 groups
impute-methodsQuantitative proteomics data imputation
iPQFiPQF: iTRAQ (and TMT) Protein Quantification based on...
isCentroidedFromFileGet mode from mzML data file
iTRAQ4iTRAQ 4-plex set
itraqdataExample 'MSnExp' and 'MSnSet' data sets
listOfTests equality of list elements class
makeCamelCaseConvert to camel case by replacing dots by captial letters
makeNaDataCreate a data with missing values
MChromatograms-classContainer for multiple Chromatogram objects
meanMzIntsCombine a list of spectra to a single spectrum
MIAPE-classThe "MIAPE" Class for Storing Proteomics Experiment...
missing-dataDocumenting missing data visualisation
MSmap-classClass 'MSmap'
MSnbaseOptionsMSnbase options
MSnExp-classThe 'MSnExp' Class for MS Data And Meta-Data
MSnProcess-classThe "MSnProcess" Class
MSnSet-classThe "MSnSet" Class for MS Proteomics Expression Data and...
MSnSetList-classStoring multiple related MSnSets
MSpectraList of Spectrum objects along with annotations
mzRident2dfrCoerce identification data to a 'data.frame'
MzTab-classParse 'MzTab' files
naplotOverview of missing value
navMSNavigate an 'MSnExp' object
nFeaturesHow many features in a group?
normalise-methodsNormalisation of 'MSnExp', 'MSnSet' and 'Spectrum' objects
normToReferenceCombine peptides into proteins.
npcvNon-parametric coefficient of variation
nQuantsCount the number of quantitfied features.
OnDiskMSnExp-classThe 'OnDiskMSnExp' Class for MS Data And Meta-Data
pickPeaks-methodPeak Detection for 'MSnExp' or 'Spectrum' instances
plot2d-methodsThe 'plot2d' method for 'MSnExp' quality assessment
plotDensity-methodsThe 'plotDensity' method for 'MSnExp' quality assessment
plot-methodsPlotting 'MSnExp' and 'Spectrum' object(s)
plotMzDelta-methodsThe delta m/z plot
plotNA-methodsExploring missing data in 'MSnSet' instances
plotSpectrumSpectrum-methodsPlotting a 'Spectrum' vs another 'Spectrum' object.
precSelectionNumber of precursor selection events
ProcessingStep-classSimple processing step class
pSet-classClass to Contain Raw Mass-Spectrometry Assays and...
purityCorrect-methodsPerforms reporter ions purity correction
quantify-methodsQuantifies 'MSnExp' and 'Spectrum' objects
readMgfDataImport mgf files as 'MSnExp' instances.
readMSDataImports mass-spectrometry raw data files as 'MSnExp'...
readMSnSetRead 'MSnSet'
readMzIdDataImport peptide-spectrum matches
readMzTabDataRead an 'mzTab' file
readMzTabData_v0.9Read an 'mzTab' file
readSRMDataRead SRM/MRM chromatographic data
reduce-data.frame-methodReduce a data.frame
removeNoId-methodsRemoves non-identified features
removePeaks-methodsRemoves low intensity peaks
removeReporters-methodsRemoves reporter ion tag peaks
ReporterIons-classThe "ReporterIons" Class
selectFeatureDataSelect feature variables of interest
smooth-methodsSmooths 'MSnExp' or 'Spectrum' instances
Spectrum1-classThe "Spectrum1" Class for MS1 Spectra
Spectrum2-classThe "Spectrum2" Class for MSn Spectra
Spectrum-classThe "Spectrum" Class
TMT6TMT 6/10-plex sets
trimMz-methodsTrims 'MSnExp' or 'Spectrum' instances
updateObject-methodsUpdate MSnbase objects
writeMgfData-methodsWrite an experiment or spectrum to an mgf file
writeMSDataWrite MS data to mzML or mzXML files
writeMzTabDataExport an MzTab object as mzTab file.
MSnbase documentation built on Jan. 23, 2021, 2 a.m.