# FDR-controlled analysis of 2D-TPP experiments

## Documentation for package ‘TPP2D’ version 1.3.0

- 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
competeModels | Compete H0 and H1 models per protein and obtain F statistic
computeFdr | Compute FDR for given F statistics based on true and null dataset
computeFstat | Compute F statistic from H1 and H0 model characteristics
computePvalFromKernelDensity | Compute p-values for given F statistics based on true and null dataset using a kernel density estimation of the bootstrapped null distribution
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
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
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
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
simulated_cell_extract_df | Example subset of a simulated 2D-TPP cell extract dataset
TPP_importCheckConfigTable | Import and chech configuration table