A B C D E F G H I L M N O P Q R S T U V W X misc
MSnbase-package | MSnbase: Base Functions and Classes for MS-based Proteomics |
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 |
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 |
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.MSnSet | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data |
as.data.frame.Spectrum | The "Spectrum" Class |
as.ExpressionSet.MSnSet | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data |
as.MIAME.MIAPE | The "MIAPE" Class for Storing Proteomics Experiment Information |
assayData-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
averageMSnSet | Generate an average 'MSnSet' |
bin | Bin 'MSnExp' or 'Spectrum' instances |
bin-method | The 'MSnExp' Class for MS Data And Meta-Data |
bin-method | The "Spectrum" Class |
bin-methods | Bin 'MSnExp' or 'Spectrum' instances |
calculateFragments | Calculate ions produced by fragmentation. |
calculateFragments-method | The "Spectrum2" Class for MSMS Spectra |
calculateFragments-method | Calculate ions produced by fragmentation. |
calculateFragments_Spectrum2 | calculate fragments from a peptide sequence for a specific Spectrum only Spectrum2 is supported yet |
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 |
chromatogram | Plots a chromatogram |
chromatogram-method | Plots a chromatogram |
chromatogram-methods | Plots a chromatogram |
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 "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 | 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 |
common | Class '"FeatComp"' |
common,methods | Class '"FeatComp"' |
common-method | Class '"FeatComp"' |
compareSpectra | Compare Spectra of an 'MSnExp' or 'Spectrum' instances |
compareSpectra-method | The 'MSnExp' 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"' |
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 |
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 |
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 | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
FeaturesOfInterest | Features of Interest |
FeaturesOfInterest-class | Features of Interest |
FeaturesOfInterest-method | Features of Interest |
FeaturesOfInterest-methods | Features of Interest |
fileName-method | Class 'MSmap' |
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 |
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 | 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 |
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. |
header | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
header-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
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 |
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 |
isEmpty-method | The "Spectrum" Class |
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 |
length | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
length-method | Features of Interest |
length-method | The "ReporterIons" Class |
length-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
listOf | Tests equality of list elements class |
log-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data |
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 |
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 | Class 'MSmap' |
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' |
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 | Class 'MSmap' |
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' |
names-method | Class '"FeatComp"' |
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. |
ncol-method | Class 'MSmap' |
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 |
npcv | Non-parametric coefficient of variation |
nQuants | Count the number of quantitfied features. |
nrow-method | Class 'MSmap' |
otherInfo-method | The "MIAPE" Class for Storing Proteomics Experiment Information |
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 |
pickPeaks | Peak Detection for 'MSnExp' or 'Spectrum' instances |
pickPeaks-method | The 'MSnExp' 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 | Class 'MSmap' |
plot-method | The 'MSnExp' Class for MS Data And Meta-Data |
plot-method | The "Spectrum" Class |
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.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 "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 |
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 |
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' |
readMSnSet2 | Read 'MSnSet' |
readMzTabData | Read an 'mzTab' file |
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 "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 |
rmFeaturesOfInterest | Features of Interest |
rmFeaturesOfInterest-method | Features of Interest |
rmFeaturesOfInterest-methods | Features of Interest |
rtime | The "Spectrum" Class |
rtime-method | Class 'MSmap' |
rtime-method | The "Spectrum" Class |
rtime-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
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 | 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 | Class Containing Measured Variables and Their Meta-Data Description for Multiplexed Experiments. |
show-method | The "ReporterIons" Class |
show-method | The "Spectrum" Class |
smooth | Smooths 'MSnExp' or 'Spectrum' instances |
smooth-method | The 'MSnExp' Class for MS Data And Meta-Data |
smooth-method | The "Spectrum" Class |
smooth-methods | Smooths 'MSnExp' or 'Spectrum' instances |
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-method | Class 'MSmap' |
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 |
unique1 | Class '"FeatComp"' |
unique1,methods | Class '"FeatComp"' |
unique1-method | Class '"FeatComp"' |
unique2 | Class '"FeatComp"' |
unique2,methods | Class '"FeatComp"' |
unique2-method | Class '"FeatComp"' |
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 |
varLabels-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
varMetadata-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
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 |
xic | Extracted ion chromatograms |
xic-method | Extracted ion chromatograms |
xic-methods | Extracted ion chromatograms |
[-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 |