Analyze thermal proteome profiling (TPP) experiments


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Documentation for package ‘TPP’ version 3.0.3

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TPP-package Thermal proteome profiling (TPP)
.onLoad Thermal proteome profiling (TPP)
analyze2DTPP Analyze 2D-TPP experiment
analyzeTPPCCR Analyze TPP-CCR experiment
analyzeTPPTR Analyze TPP-TR experiment
hdacCCR_config The configuration table to analyze hdacCCR_data.
hdacCCR_data TPP-CCR example dataset (replicates 1 and 2)
hdacCCR_smallExample Example subsets of a Panobinostat TPP-CCR dataset (replicates 1 and 2) and the corresponding configuration table to start the analysis.
hdacTR_config The configuration table to analyze hdacTR_data.
hdacTR_data TPP-TR example dataset.
hdacTR_resultsTable_smallExample Example of a TPP-TR result table.
hdacTR_smallExample Example subset of a Panobinostat TPP-TR dataset and the corresponding configuration table to start the analysis.
panob2D_isobQuant_example Example subsets of a Panobinostat 2D-TPP dataset and the corresponding configuration table to start the analysis.
panobinostat_2DTPP_config The configuration table to analyze panobinostat_2DTPP_data.
panobinostat_2DTPP_data 2D-TPP-CCR example dataset
resultTable Example of a TPP-TR result table.
TPP Thermal proteome profiling (TPP)
tpp2dAddAdditionalInfo Add additional info to 2D-TPP CCR output data
tpp2dCalcFractAbundance Calculate fractional abundance and DMSO ratio of successive sumionareas (usage of function is only reasonable when at least two temperatures are multiplexed!)
tpp2dComputeFoldChanges Compute 2D-TPP fold changes
tpp2dCreateCCRConfigFile Create TPP-CCR config files for 2D-TPP experiment
tpp2dCreateDataFrameList Create data frame list for 2D-TPP experiment
tpp2dCreateReport Create Report of 2D-TPP analysis
tpp2dCreateTPPTRreference Create TPP-TR reference for 2D-TPP experiment
tpp2dCurveFit Run TPP-CCR analysis for 2D-TPP experiment
tpp2dEvalConfigTable Evaluation of 2D-TPP Configuration File
tpp2dExport Produce Excel table of 2D-TPP experiment.
tpp2dExportPlots Export plots for 2D-TPP experiment.
tpp2dImport Import 2D-TPP data
tpp2dMerge2dRef Merge 2D-TPP result data with TPP-TR reference data
tpp2dNormalize Median normalization of protein fold changes of 2D-TPP data
tpp2dPlotCCRAllCurves Plot all 2D-TPP CCR curves
tpp2dPlotCCRGoodCurves Plot 2D-TPP CCR curves meeting the requirements
tpp2dPlotCCRSingleCurves Plot single 2D-TPP CCR curves
tpp2dPlotQChist Plot quality control histograms
tpp2dPlotQCpEC50 Plot quality control pEC50 plots
tpp2dRemoveNAs Remove NAs in 2D-TPP data
tpp2dRemoveZeroSias Remove rows with zero sumionarea values
tpp2dReplaceColNames Replace column names for 2D-TPP data
tpp2dSplineFitAndTest Fit splines and perform f-Test
tpp2dSplinePlot Fit splines and generate ggplot visualizations
tpp2dTRReferenceObject TPP-TR reference object
tppccrCurveFit Fit dose response curves
tppccrImport Import TPP-CCR dataset for analysis by the 'TPP' package.
tppccrNormalize Normalize data from TPP-CCR experiments
tppccrNormalizeToReference Normalize fold changes of TPP-CCR experiment to a reference column
tppccrPlotCurves Plot dose response curves
tppccrResultTable Summarize results of a TPP-CCR study
tppccrTransform Transform fold changes of TPP-CCR experiment
tppDefaultTheme Default ggplot theme for melting curve plots.
tppExport Produce Excel table of TPP-TR or TPP-CCR experiment.
tppQCPlotsCorrelateExperiments Visually compare fold changes of different TPP experiments.
tpptrAnalyzeMeltingCurves Analyze fitted curve parameters to detect significant shifts in melting points.
tpptrCurveFit Fit melting curves to all proteins in a dataset.
tpptrDefaultNormReqs Default filter criteria for fold change normalization
tpptrFitSplines Perform spline fitting
tpptrFTest Analyze spline fits to detect differential behavior over time
tpptrImport Import TPP-TR datasets for analysis by the 'TPP' package.
tpptrNormalize Normalize protein fold changes
tpptrPlotSplines Plot spline fits per protein
tpptrSplineFitAndTest Perform spline fitting and analyze by moderated F-test
tpptrTidyUpESets Tidy up expressionSets