Package index • einprot

All functions
`addSampleAnnots()`	Add sample annotations to SummarizedExperiment object
`combineIds()`	Combine multiple columns into a new column
`EINPROT_COMPLEXES_FILE` `EINPROT_WORMBASE_CONVTABLE` `EINPROT_POMBASE_CONVTABLE`	Constants
`defineAssayNames()`	Define assay names
`doImputation()`	Perform imputation of NA values
`doNormalization()`	Apply normalization
`doPCA()`	Run PCA and generate plots
`filterFragPipe()`	Filter out features in FragPipe data
`filterMaxQuant()`	Filter out features in MaxQuant data
`filterPDTMT()`	Filter out features in PD/TMT data
`filterSpectronaut()`	Filter out features in Spectronaut data
`fixFeatureIds()`	Define various ID columns
`formatTableColumns()`	Format table columns
`getColumnNames()`	Get column names
`getConvTable()`	Download and process conversion tables
`getIntensityColumns()`	Extract intensity columns from intensity file
`getMatSubtractedBaseline()`	Extract a matrix and subtract the background/baseline for each feature
`getFirstId()` `getNthId()`	Extract feature identifiers
`getSpeciesInfo()`	Get species info
`getSupportedSpecies()`	List supported species
`getUniProtToIDMapping()`	Get mapping from UniProt IDs to another ID type
`importDIANN()`	Import data from DIA-NN into a SingleCellExperiment object
`importExperiment()`	Import an abundance file
`importSpectronaut()`	Import data from Spectronaut into a SingleCellExperiment object
`listComplexDBs()`	List available complex DBs
`makeAbundanceExport()`	Assemble table with abundances of significant features
`makeAbundanceHeatmap()`	Generate heatmap
`makeComplexDB()`	Generate a comprehensive database of complexes
`makeDbLinkTable()`	Make table with database links
`makeIntensityBoxplots()`	Make intensity boxplot
`makeListOfComparisons()`	Compile a list of comparisons
`makeMeanSDPlot()`	Make mean-vs-SD plot
`makeSAPlot()`	Construct SA plot from limma results
`makeTableFromList()`	Make table from list
`makeiSEEScript()`	Compile an R script for launching an adapted `iSEE` instance
`plotDetectedInSamples()`	Plot feature detection rate
`plotFractionDetectedPerSample()`	Plot detection rate per sample
`plotImputationDistribution()`	Plot distribution of imputed and unimputed values
`plotMissingValuesHeatmap()`	Plot heatmap of missing values
`plotVolcano()`	Make volcano plots
`prepareFeatureCollections()`	Prepare feature collections for testing with camera
`prepareFinalSCE()`	Prepare SingleCellExperiment for use with iSEE
`getContaminantsDatabaseFrompdAnalysis()` `getSearchParametersFrompdAnalysis()` `getMaxMissedCleavagesFrompdAnalysis()` `getQuantOrderFrompdAnalysis()` `getTemplateNamesFrompdAnalysis()` `getValidationInfoFrompdAnalysis()` `getPSMValidationInfoFrompdAnalysis()` `getCalibrationFrompdAnalysis()` `getQuantInfoFrompdAnalysis()`	Extract information from a pdAnalysis file
`readDIANNInfo()`	Extract information from DIA-NN logs
`readFragPipeInfo()`	Extract information from FragPipe logs
`readMaxQuantXML()`	Extract information from MaxQuant logs
`readProteomeDiscovererInfo()`	Extract information from Proteome Discoverer logs
`readSpectronautSetup()`	Extract information from Spectronaut setup file
`runDIANNAnalysis()`	Run analysis on DIA-NN data
`runFragPipeAnalysis()`	Run analysis on FragPipe data
`runMaxQuantAnalysis()`	Run analysis on MaxQuant data
`runPDTMTAnalysis()`	Run analysis on PD/TMT data
`runPDTMTptmAnalysis()`	Run PTM analysis on PD/TMT data
`runPTMTest()`	Perform PTM test
`runSpectronautAnalysis()`	Run analysis on Spectronaut data
`runTest()`	Run statistical test
`seqLogoApp()`	Generate a shiny app to explore sequence logos
`emptySampleText()` `testText()` `normText()` `saText()` `expDesignText()` `introText()` `filterByModText()` `inputText()`	Text snippets for use in analysis reports

Reference

All functions