![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
| annotateDataList | Annotate imported data list using a config table |
| bootstrapNull | Bootstrap null distribution of F statistics for FDR estimation |
| bootstrapNullAlternativeModel | Bootstrap null distribution of F statistics for FDR estimation based on resampling alternative model residuals |
| competeModels | Compete H0 and H1 models per protein and obtain F statistic |
| computeFstat | Compute F statistic from H1 and H0 model characteristics |
| computeFStatFromParams | Compute F statistics from paramter data frame |
| configWide2Long | Tranform configuration table from wide to long |
| config_tab | Example config table for a import of a simulated 2D-TPP cell extract dataset |
| filterOutContaminants | Filter out contaminants |
| findHits | Find hits according to FDR threshold |
| fitAndEvalDataset | Fit H0 and H1 model to 2D thermal profiles of proteins and compute F statistic |
| fitH0Model | Fit H0 model and evaluate fit statistics |
| fitH1Model | Fit H1 model and evaluate fit statistics |
| getFDR | Get FDR for given F statistics based on true and null dataset |
| getModelParamsDf | Get H0 and H1 model parameters |
| getPEC504Temperature | Get pEC50 for a protein of interest at a specific temperatures (optimally the melting point of the protein) |
| getPvalues | Compute p-values for given F statistics based on true and null dataset |
| gg_qq | Plot qq-plot of true data and bootstrapped null with ggplot |
| import2dDataset | Import 2D-TPP dataset using a config table |
| import2dMain | Import 2D-TPP dataset main function |
| plot2dTppFcHeatmap | Plot heatmap of 2D thermal profile fold changes of a protein of choice |
| plot2dTppFit | Plot H0 or H1 fit of 2D thermal profile intensities of a protein of choice |
| plot2dTppProfile | Plot 2D thermal profile intensities of a protein of choice |
| plot2dTppRelProfile | Plot 2D thermal profile ratios of a protein of choice |
| plot2dTppVolcano | Plot Volcano plot of TPP2D results |
| raw_dat_list | Example raw data for a subset of a simulated 2D-TPP cell extract dataset |
| recomputeSignalFromRatios | Recompute robust signal intensities based on bootstrapped TMT channel ratios |
| renameColumns | Rename columns of imported data frame |
| resolveAmbiguousProteinNames | Resolve ambiguous protein names |
| runTPP2D | Run complete TPP2D analysis |
| simulated_cell_extract_df | Example subset of a simulated 2D-TPP cell extract dataset |
| tpcaResult | S4 TPP2D Experiment Class |
| tpp2dExperiment-class | S4 TPP2D Experiment Class |
| TPP_importCheckConfigTable | Import and chech configuration table |