FDR-controlled analysis of 2D-TPP experiments


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Documentation for package ‘TPP2D’ version 1.0.0

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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
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