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-methodsPlots a chromatogram
clean-methodsCleans 'MSnExp' or 'Spectrum' instances
combineFeaturesCombines features in an 'MSnSet' object
commonFeatureNamesKeep only common feature names
compareMSnSetsCompare two MSnSets
compareSpectra-methodsCompare Spectra of an 'MSnExp' or 'Spectrum' instances
defunctMSnbase Deprecated and Defunct
estimateNoise-methodNoise Estimation for 'Spectrum' instances
exprsToRatios-methodsCalculate all ratio pairs
extractPrecSpectra-methodsExtracts precursor-specific spectra from an 'MSnExp' object
FeatComp-classClass '"FeatComp"'
featureCVCalculates coeffivient of variation for features
FeaturesOfInterest-classFeatures of Interest
fillUpFills up a vector
formatRtFormat Retention Time
get.amino.acidsAmino acids
get.atomic.massAtomic mass.
getVariableNameReturn a variable name
grepEcolsReturns the matching column names of indices.
imageNA2NA heatmap visualisation for 2 groups
impute-methodsQuantitative proteomics data imputation
iPQFiPQF: iTRAQ (and TMT) Protein Quantification based on...
iTRAQ4iTRAQ 4-plex set
itraqdataExample 'MSnExp' and 'MSnSet' data sets
listOfTests equality of list elements class
makeNaDataCreate a data with missing values
MIAPE-classThe "MIAPE" Class for Storing Proteomics Experiment...
missing-dataDocumenting missing data visualisation
MSmap-classClass 'MSmap'
MSnbaseOptionsMSnbase options
MSnbase-packageMSnbase: Base Functions and Classes for MS-based Proteomics
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
MzTab-classParse 'MzTab' files
NAnnotatedDataFrame-classClass Containing Measured Variables and Their Meta-Data...
naplotOverview of missing value
navMSNavigate an 'MSnExp' object
nFeaturesHow many features in a group?
normalise-methodsNormalisation of 'MSnExp', 'MSnSet' and 'Spectrum' objects
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 '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'
readMzTabDataRead an 'mzTab' file
readMzTabData_v0.9Read an 'mzTab' file
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
xic-methodsExtracted ion chromatograms
MSnbase documentation built on May 31, 2017, 11:06 a.m.