A B C D E F G H I L M N O P Q R S T U V W misc
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 "MSnSet" Class for MS Proteomics Expression Data and Meta-Data |
acquisitionNum-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
acquisitionNum-method | List of Spectrum objects along with annotations |
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 |
addMSnSetMetadata | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data |
aggregationFun | Representation of chromatographic MS data |
aggvar | Identify aggregation outliers |
all.equal-method | The 'MSnExp' Class for MS Data And Meta-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 | Coerce identification data to a 'data.frame' |
as.data.frame-method | Representation of chromatographic MS data |
as.data.frame.MSnExp | The 'MSnExp' Class for MS Data And Meta-Data |
as.data.frame.MSnSet | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data |
as.data.frame.mzRident | Coerce identification data to a 'data.frame' |
as.data.frame.Spectrum | The "Spectrum" Class |
as.ExpressionSet.MSnSet | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data |
as.matrix.FoICollection | Features of Interest |
as.MIAME.MIAPE | The "MIAPE" Class for Storing Proteomics Experiment Information |
as.MSnExp.OnDiskMSnExp | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
as.MSnSet.ExpressionSet | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data |
assayData-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
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 | Representation of chromatographic MS data |
bin-method | Container for multiple Chromatogram objects |
bin-method | The 'MSnExp' Class for MS Data And Meta-Data |
bin-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
bin-method | The "Spectrum" Class |
bin-methods | Bin 'MSnExp' or 'Spectrum' instances |
bpi | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
bpi-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
calculateFragments | Calculate ions produced by fragmentation. |
calculateFragments-method | The "Spectrum2" Class for MSn Spectra |
calculateFragments-method | Calculate ions produced by fragmentation. |
centroided | The "Spectrum" Class |
centroided-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
centroided-method | List of Spectrum objects along with annotations |
centroided-method | The "Spectrum" Class |
centroided-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
centroided<- | The "Spectrum" Class |
centroided<--method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
centroided<--method | The "Spectrum" Class |
centroided<--method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
Chromatogram | Representation of chromatographic MS data |
chromatogram | Extract chromatogram object(s) |
Chromatogram-class | Representation of chromatographic MS data |
chromatogram-method | Extract chromatogram object(s) |
Chromatograms | Container for multiple Chromatogram objects |
Chromatograms-class | Container for multiple Chromatogram objects |
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:MzTab | Parse 'MzTab' files |
class:OnDiskMSnExp | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
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 MSn Spectra |
clean | Clean 'MSnExp', 'Spectrum' or 'Chromatogram' instances |
clean-method | Representation of chromatographic MS data |
clean-method | Container for multiple Chromatogram objects |
clean-method | The 'MSnExp' Class for MS Data And Meta-Data |
clean-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
clean-method | List of Spectrum objects along with annotations |
clean-method | The "Spectrum" Class |
clean-methods | Clean 'MSnExp', 'Spectrum' or 'Chromatogram' instances |
coerce-method | Container for multiple Chromatogram objects |
coerce-method | Features of Interest |
coerce-method | The "MIAPE" Class for Storing Proteomics Experiment Information |
coerce-method | Class 'MSmap' |
coerce-method | The 'MSnExp' Class for MS Data And Meta-Data |
coerce-method | The "MSnProcess" Class |
coerce-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data |
coerce-method | Parse 'MzTab' files |
coerce-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
coerce-method | List of Spectrum objects along with annotations |
coerce-method | The "Spectrum" Class |
coerce-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
coerce-method | Import peptide-spectrum matches |
collisionEnergy | The "Spectrum2" Class for MSn Spectra |
collisionEnergy-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
collisionEnergy-method | List of Spectrum objects along with annotations |
collisionEnergy-method | The "Spectrum2" Class for MSn Spectra |
collisionEnergy-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
colnames<--method | Container for multiple Chromatogram objects |
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 |
combineSpectra | Combine Spectra |
combineSpectra-method | Combine Spectra |
combineSpectraMovingWindow | Combine signal from consecutive spectra of LCMS experiments |
comments | Parse 'MzTab' files |
common | Class '"FeatComp"' |
common,methods | Class '"FeatComp"' |
common-method | Class '"FeatComp"' |
commonFeatureNames | Keep only common feature names |
compareMSnSets | Compare two MSnSets |
compareSpectra | Compare Spectra of an 'MSnExp' or 'Spectrum' instances |
compareSpectra-method | The 'MSnExp' Class for MS Data And Meta-Data |
compareSpectra-method | The 'OnDiskMSnExp' 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"' |
consensusSpectrum | Combine spectra to a consensus spectrum |
defaultNeutralLoss | Calculate ions produced by fragmentation. |
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 to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
droplevels.MSnSet | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data |
estimateMzResolution | Estimate the m/z resolution of a spectrum |
estimateMzResolution-method | Estimate the m/z resolution of a spectrum |
estimateMzScattering | Estimate m/z scattering in consecutive scans |
estimateNoise | Noise Estimation for 'Spectrum' instances |
estimateNoise-method | The 'MSnExp' Class for MS Data And Meta-Data |
estimateNoise-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
estimateNoise-method | The "Spectrum" Class |
estimateNoise-methods | Noise Estimation for 'Spectrum' instances |
executeProcessingStep | Simple processing step class |
expandFeatureVars | Expand or merge feature variables |
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 |
exprs-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data |
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-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
extractPrecSpectra-methods | Extracts precursor-specific spectra from an 'MSnExp' object |
factorsAsStrings | Converts factors to strings |
fData-method | Container for multiple Chromatogram objects |
fData-method | Storing multiple related MSnSets |
fData-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
fData<--method | Container for multiple Chromatogram objects |
fData<--method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data |
fData<--method | Storing multiple related MSnSets |
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 | Container for multiple Chromatogram objects |
featureData-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
featureData<--method | Container for multiple Chromatogram objects |
featureNames-method | Container for multiple Chromatogram objects |
featureNames-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
featureNames-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
featureNames<--method | Container for multiple Chromatogram objects |
featureNames<--method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
FeaturesOfInterest | Features of Interest |
FeaturesOfInterest-class | Features of Interest |
FeaturesOfInterest-method | Features of Interest |
FeaturesOfInterest-methods | Features of Interest |
fileName-method | Class 'MSmap' |
fileName-method | Parse 'MzTab' files |
fileNames | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
fileNames-method | Class 'MSmap' |
fileNames-method | The "MSnProcess" Class |
fileNames-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data |
fileNames-method | Parse 'MzTab' files |
fileNames-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
fillUp | Fills up a vector |
filterAcquisitionNum | The 'MSnExp' Class for MS Data And Meta-Data |
filterAcquisitionNum-method | The 'MSnExp' Class for MS Data And Meta-Data |
filterEmptySpectra | The 'MSnExp' Class for MS Data And Meta-Data |
filterEmptySpectra-method | The 'MSnExp' Class for MS Data And Meta-Data |
filterFile | The 'MSnExp' Class for MS Data And Meta-Data |
filterFile-method | The 'MSnExp' Class for MS Data And Meta-Data |
filterIdentificationDataFrame | Filter out unreliable PSMs. |
filterIsolationWindow | The 'MSnExp' Class for MS Data And Meta-Data |
filterIsolationWindow-method | The 'MSnExp' Class for MS Data And Meta-Data |
filterMsLevel | The 'MSnExp' Class for MS Data And Meta-Data |
filterMsLevel-method | The 'MSnExp' Class for MS Data And Meta-Data |
filterMsLevel-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data |
filterMsLevel-method | List of Spectrum objects along with annotations |
filterMz | Trims 'MSnExp' or 'Spectrum' instances |
filterMz-method | The 'MSnExp' Class for MS Data And Meta-Data |
filterMz-method | List of Spectrum objects along with annotations |
filterMz-method | The "Spectrum" Class |
filtermz-method | The "Spectrum" Class |
filterMz-methods | Trims 'MSnExp' or 'Spectrum' instances |
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 |
filterPolarity | The 'MSnExp' Class for MS Data And Meta-Data |
filterPolarity-method | The 'MSnExp' Class for MS Data And Meta-Data |
filterPrecursorMz | The 'MSnExp' Class for MS Data And Meta-Data |
filterPrecursorMz-method | The 'MSnExp' Class for MS Data And Meta-Data |
filterPrecursorScan | The 'MSnExp' Class for MS Data And Meta-Data |
filterPrecursorScan-method | The 'MSnExp' Class for MS Data And Meta-Data |
filterRt | The 'MSnExp' Class for MS Data And Meta-Data |
filterRt-method | Representation of chromatographic MS data |
filterRt-method | The 'MSnExp' Class for MS Data And Meta-Data |
filterZero | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data |
filterZero-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 | Representation of chromatographic MS data |
fromFile-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data |
fromFile-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
fromFile-method | List of Spectrum objects along with annotations |
fromFile-method | The "Spectrum" Class |
fromFile-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
fvarLabels-method | Container for multiple Chromatogram objects |
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. |
hasChromatograms | Checks if raw data files have any spectra or chromatograms |
hasSpectra | Checks if raw data files have any spectra or chromatograms |
header | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
header-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
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 |
image2 | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data |
imageNA2 | NA heatmap visualisation for 2 groups |
impute | Quantitative proteomics data imputation |
impute-method | Quantitative proteomics data imputation |
impute-methods | Quantitative proteomics data imputation |
imputeMethods | 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 | Representation of chromatographic MS data |
intensity-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
intensity-method | List of Spectrum objects along with annotations |
intensity-method | The "Spectrum" Class |
intensity-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
ionCount | The "Spectrum" Class |
ionCount-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
ionCount-method | List of Spectrum objects along with annotations |
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 |
iPQF | iPQF: iTRAQ (and TMT) Protein Quantification based on Features |
is.na.MSnSet | Exploring missing data in 'MSnSet' instances |
isCentroided | The "Spectrum" Class |
isCentroided-method | The 'MSnExp' Class for MS Data And Meta-Data |
isCentroided-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
isCentroided-method | List of Spectrum objects along with annotations |
isCentroided-method | The "Spectrum" Class |
isCentroidedFromFile | Get mode from mzML data file |
isEmpty-method | Representation of chromatographic MS data |
isEmpty-method | Container for multiple Chromatogram objects |
isEmpty-method | List of Spectrum objects along with annotations |
isEmpty-method | The "Spectrum" Class |
isMSnbaseFastLoad | MSnbase options |
isMSnbaseVerbose | MSnbase options |
isolationWindow-method | The 'MSnExp' Class for MS Data And Meta-Data |
isolationWindowLowerMz | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
isolationWindowLowerMz-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
isolationWindowLowerMz-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
isolationWindowUpperMz | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
isolationWindowUpperMz-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
isolationWindowUpperMz-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
iTRAQ4 | iTRAQ 4-plex set |
iTRAQ5 | iTRAQ 4-plex set |
iTRAQ8 | iTRAQ 4-plex set |
iTRAQ9 | iTRAQ 4-plex set |
itraqdata | Example 'MSnExp' and 'MSnSet' data sets |
lapply-method | Storing multiple related MSnSets |
length | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
length-method | Representation of chromatographic MS data |
length-method | Features of Interest |
length-method | Storing multiple related MSnSets |
length-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
length-method | The "ReporterIons" Class |
length-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
lengths-method | Features of Interest |
listOf | Tests equality of list elements class |
log-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data |
makeCamelCase | Convert to camel case by replacing dots by captial letters |
makeImpuritiesMatrix | Performs reporter ions purity correction |
makeNaData | Create a data with missing values |
makeNaData2 | Create a data with missing values |
MAplot-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data |
meanMzInts | Combine a list of spectra to a single spectrum |
meanSdPlot-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data |
mergeFeatureVars | Expand or merge feature variables |
metadata-method | Parse 'MzTab' files |
MIAPE | The "MIAPE" Class for Storing Proteomics Experiment Information |
MIAPE-class | The "MIAPE" Class for Storing Proteomics Experiment Information |
missing-data | Documenting missing data visualisation |
missingdata | Documenting missing data visualisation |
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 | Representation of chromatographic MS data |
msLevel-method | Class 'MSmap' |
msLevel-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
msLevel-method | List of Spectrum objects along with annotations |
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' |
msMap-method | Class 'MSmap' |
MSnbaseOptions | MSnbase options |
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 | Example 'MSnExp' and 'MSnSet' data sets |
MSnSet-class | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data |
msnset2 | Example 'MSnExp' and 'MSnSet' data sets |
MSnSetList | Storing multiple related MSnSets |
MSnSetList-class | Storing multiple related MSnSets |
msnsets | Storing multiple related MSnSets |
mz | The "Spectrum" Class |
mz-method | Representation of chromatographic MS data |
mz-method | Container for multiple Chromatogram objects |
mz-method | Class 'MSmap' |
mz-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
mz-method | The "ReporterIons" Class |
mz-method | List of Spectrum objects along with annotations |
mz-method | The "Spectrum" Class |
mz-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
mzRes | Class 'MSmap' |
mzRes-method | Class 'MSmap' |
MzTab | Parse 'MzTab' files |
MzTab-class | Parse 'MzTab' files |
mzTabMode | Parse 'MzTab' files |
mzTabType | Parse 'MzTab' files |
names-method | Class '"FeatComp"' |
names-method | Features of Interest |
names-method | Storing multiple related MSnSets |
names-method | The "ReporterIons" Class |
names<--method | Features of Interest |
names<--method | Storing multiple related MSnSets |
naplot | Overview of missing value |
naset | Quantitative proteomics data imputation |
navMS | Navigate an 'MSnExp' object |
ncol-method | Class 'MSmap' |
nextMS | Navigate an 'MSnExp' object |
nFeatures | How many features in a group? |
normalise | Normalisation of 'MSnExp', 'MSnSet' and 'Spectrum' objects |
normalise-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
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 | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
normalize-method | Normalisation of 'MSnExp', 'MSnSet' and 'Spectrum' objects |
normalize-methods | Normalisation of 'MSnExp', 'MSnSet' and 'Spectrum' objects |
normToReference | Combine peptides into proteins. |
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' |
NTR | Combine peptides into proteins. |
objlog | Storing multiple related MSnSets |
OnDiskMSnExp | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
OnDiskMSnExp-class | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
otherInfo-method | The "MIAPE" Class for Storing Proteomics Experiment Information |
pData-method | Container for multiple Chromatogram objects |
pData-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
pData<--method | Container for multiple Chromatogram objects |
pData<--method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data |
pData<--method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
peaksCount | The "Spectrum" Class |
peaksCount-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
peaksCount-method | List of Spectrum objects along with annotations |
peaksCount-method | The "Spectrum" Class |
peaksCount-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
peptides-method | Parse 'MzTab' files |
phenoData-method | Container for multiple Chromatogram objects |
phenoData-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 'OnDiskMSnExp' Class for MS Data And Meta-Data |
pickPeaks-method | List of Spectrum objects along with annotations |
pickPeaks-method | The "Spectrum" Class |
pickPeaks-methods | Peak Detection for 'MSnExp' or 'Spectrum' instances |
plot | Plotting 'MSnExp' and 'Spectrum' object(s) |
plot,MSnExp | The 'MSnExp' Class for MS Data And Meta-Data |
plot-method | Representation of chromatographic MS data |
plot-method | Container for multiple Chromatogram objects |
plot-method | Class 'MSmap' |
plot-method | The 'MSnExp' Class for MS Data And Meta-Data |
plot-method | Plotting 'MSnExp' and 'Spectrum' object(s) |
plot-method | Plotting a 'Spectrum' vs another 'Spectrum' object. |
plot-methods | Plotting 'MSnExp' and 'Spectrum' object(s) |
plot.MSnExp | Plotting 'MSnExp' and 'Spectrum' object(s) |
plot.Spectrum | Plotting 'MSnExp' and 'Spectrum' object(s) |
plot.Spectrum.character | Plotting 'MSnExp' and '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 "Spectrum" Class |
polarity-method | Container for multiple Chromatogram objects |
polarity-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
polarity-method | List of Spectrum objects along with annotations |
polarity-method | The "Spectrum" Class |
polarity-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
precAcquisitionNum | The "Spectrum2" Class for MSn Spectra |
precAcquisitionNum-method | The "Spectrum2" Class for MSn Spectra |
precAcquisitionNum-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
precScanNum | The "Spectrum2" Class for MSn Spectra |
precScanNum-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
precScanNum-method | List of Spectrum objects along with annotations |
precScanNum-method | The "Spectrum2" Class for MSn 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 MSn Spectra |
precursorCharge-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
precursorCharge-method | List of Spectrum objects along with annotations |
precursorCharge-method | The "Spectrum2" Class for MSn Spectra |
precursorCharge-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
precursorIntensity | The "Spectrum2" Class for MSn Spectra |
precursorIntensity-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
precursorIntensity-method | List of Spectrum objects along with annotations |
precursorIntensity-method | The "Spectrum2" Class for MSn Spectra |
precursorIntensity-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
precursorMz | The "Spectrum2" Class for MSn Spectra |
precursorMz-method | Representation of chromatographic MS data |
precursorMz-method | Container for multiple Chromatogram objects |
precursorMz-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
precursorMz-method | List of Spectrum objects along with annotations |
precursorMz-method | The "Spectrum2" Class for MSn Spectra |
precursorMz-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
prevMS | Navigate an 'MSnExp' object |
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 |
ProcessingStep | Simple processing step class |
ProcessingStep-class | Simple processing step class |
ProcessingStep:OnDiskMSnExp | Simple processing step class |
productMz | Representation of chromatographic MS data |
productMz-method | Representation of chromatographic MS data |
productMz-method | Container for multiple Chromatogram objects |
proteins-method | Parse 'MzTab' files |
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 |
psms-method | Parse 'MzTab' files |
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 'OnDiskMSnExp' Class for MS Data And Meta-Data |
quantify-method | The "Spectrum" Class |
quantify-methods | Quantifies 'MSnExp' and 'Spectrum' objects |
readMgfData | Import mgf files as 'MSnExp' instances. |
readMSData | Imports mass-spectrometry raw data files as 'MSnExp' instances. |
readMSData2 | Imports mass-spectrometry raw data files as 'MSnExp' instances. |
readMSnSet | Read 'MSnSet' |
readMSnSet2 | Read 'MSnSet' |
readMzIdData | Import peptide-spectrum matches |
readMzTabData | Read an 'mzTab' file |
readMzTabData_v0.9 | Read an 'mzTab' file |
readSRMData | Read SRM/MRM chromatographic data |
reduce-method | Reduce a data.frame |
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 'OnDiskMSnExp' Class for MS Data And Meta-Data |
removePeaks-method | List of Spectrum objects along with annotations |
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 MSn 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 |
requiredFvarLabels | Select feature variables of interest |
rmFeaturesOfInterest | Features of Interest |
rmFeaturesOfInterest-method | Features of Interest |
rmFeaturesOfInterest-methods | Features of Interest |
rownames<--method | Container for multiple Chromatogram objects |
rtime | The "Spectrum" Class |
rtime-method | Representation of chromatographic MS data |
rtime-method | Class 'MSmap' |
rtime-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
rtime-method | List of Spectrum objects along with annotations |
rtime-method | The "Spectrum" Class |
rtime-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
sampleNames-method | Container for multiple Chromatogram objects |
sampleNames-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
sampleNames<--method | Container for multiple Chromatogram objects |
sampleNames<--method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
samples-method | The "MIAPE" Class for Storing Proteomics Experiment Information |
sapply-method | Storing multiple related MSnSets |
scale-method | Normalisation of 'MSnExp', 'MSnSet' and 'Spectrum' objects |
scanIndex | The "Spectrum" Class |
scanIndex-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
scanIndex-method | List of Spectrum objects along with annotations |
scanIndex-method | The "Spectrum" Class |
scanIndex-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
selectFeatureData | Select feature variables of interest |
setMSnbaseFastLoad | MSnbase options |
setMSnbaseParallelThresh | MSnbase options |
setMSnbaseVerbose | MSnbase options |
show-method | Representation of chromatographic MS data |
show-method | Container for multiple Chromatogram objects |
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 | Storing multiple related MSnSets |
show-method | Parse 'MzTab' files |
show-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
show-method | Simple processing step class |
show-method | The "ReporterIons" Class |
show-method | List of Spectrum objects along with annotations |
show-method | The "Spectrum" Class |
smallMolecules | Parse 'MzTab' files |
smooth | Smooths 'MSnExp' or 'Spectrum' instances |
smooth-method | The 'MSnExp' Class for MS Data And Meta-Data |
smooth-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
smooth-method | List of Spectrum objects along with annotations |
smooth-method | The "Spectrum" Class |
smooth-methods | Smooths 'MSnExp' or 'Spectrum' instances |
smoothed | The "Spectrum" Class |
smoothed-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
smoothed-method | List of Spectrum objects along with annotations |
smoothed-method | The "Spectrum" Class |
smoothed-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
smoothed<- | The "Spectrum" Class |
smoothed<--method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
smoothed<--method | The "Spectrum" Class |
smoothed<--method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
Spectra | List of Spectrum objects along with annotations |
spectra | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
Spectra-class | List of Spectrum objects along with annotations |
spectra-method | The 'MSnExp' Class for MS Data And Meta-Data |
spectra-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
spectra-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
spectrapply | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
spectrapply-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
spectrapply-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 MSn Spectra |
Spectrum2-class | The "Spectrum2" Class for MSn Spectra |
split-method | Storing multiple related MSnSets |
splitByFile | The 'MSnExp' Class for MS Data And Meta-Data |
splitByFile-method | The 'MSnExp' Class for MS Data And Meta-Data |
t-method | Class 'MSmap' |
t.MSnSet | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data |
tic | The "Spectrum" Class |
tic-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
tic-method | List of Spectrum objects along with annotations |
tic-method | The "Spectrum" Class |
tic-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
TMT10 | TMT 6/10-plex sets |
TMT10ETD | TMT 6/10-plex sets |
TMT10HCD | TMT 6/10-plex sets |
TMT11 | TMT 6/10-plex sets |
TMT11HCD | TMT 6/10-plex sets |
TMT6 | TMT 6/10-plex sets |
TMT6b | TMT 6/10-plex sets |
TMT7 | TMT 6/10-plex sets |
TMT7b | TMT 6/10-plex sets |
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 'OnDiskMSnExp' Class for MS Data And Meta-Data |
trimMz-method | The "Spectrum" Class |
trimMz-methods | Trims 'MSnExp' or 'Spectrum' instances |
trimws | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data |
trimws-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data |
unique1 | Class '"FeatComp"' |
unique1,methods | Class '"FeatComp"' |
unique1-method | Class '"FeatComp"' |
unique2 | Class '"FeatComp"' |
unique2,methods | Class '"FeatComp"' |
unique2-method | Class '"FeatComp"' |
unsplit-method | Storing multiple related MSnSets |
updateFeatureNames | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data |
updateFvarLabels | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data |
updateObject-method | Update MSnbase objects |
updateSampleNames | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data |
validateOnDiskMSnExp | The 'OnDiskMSnExp' Class for MS 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 |
whichNA | Create a data with missing values |
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 | List of Spectrum objects along with annotations |
writeMgfData-method | Write an experiment or spectrum to an mgf file |
writeMgfData-methods | Write an experiment or spectrum to an mgf file |
writeMSData | Write MS data to mzML or mzXML files |
writeMSData-method | Write MS data to mzML or mzXML files |
$-method | Container for multiple Chromatogram objects |
$-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
$<--method | Container for multiple Chromatogram objects |
$<--method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
[-method | Container for multiple Chromatogram objects |
[-method | Features of Interest |
[-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data |
[-method | Storing multiple related MSnSets |
[-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
[-method | The "ReporterIons" Class |
[-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
[<--method | Container for multiple Chromatogram objects |
[[-method | Features of Interest |
[[-method | Storing multiple related MSnSets |
[[-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
[[-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |