# Detection of ligand-protein interactions from 2D thermal profiles (DLPTP)

## Documentation for package ‘TPP2D’ version 1.21.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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
bootstrapNullAlternativeModelFast | Bootstrap null distribution of F statistics for FDR estimation based on resampling alternative model residuals with only one round of model fitting on resampled data and subsequent resampling of thereby obtained 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