tppccrResultTable: Summarize results of a TPP-CCR study
In TPP: Analyze thermal proteome profiling (TPP) experiments

Description Usage Arguments Value See Also Examples

tppccrResultTable summarizes the outcomes of a TPP-CCR study in a results table and includes quality information about the estimated dose response curves.

1	tppccrResultTable(data, r2Cutoff = 0.8)

data

list of expressionSet objects containing protein fold changes, as well as fitted curve parameters.

r2Cutoff

quality criterion on dose response curve fit.

@details data is a list of expressionSet objects created by tppccrCurveFit or tppccrPlotCurves. It contains the isobaric labels and administered drug concentrations in the phenoData and user-defined protein properties (including dose response curve parameters) in the featureData. Protein IDs are stored in the featureNames.

If data is the output of tppccrPlotCurves, plot locations are given in the plot column of the featureData.

A data frame in which the results are stored row-wise for each protein, together with the original annotation from the input files.

tppccrCurveFit,tppccrPlotCurves

data(hdacCCR_smallExample)
tppccrData <- tppccrImport(configTable=hdacCCR_config, 
                           data=hdacCCR_data)
tppccrNorm <- tppccrNormalize(data=tppccrData)
tppccrTransformed <- tppccrTransform(data=tppccrNorm)
tppccrFitted <- tppccrCurveFit(data=tppccrTransformed, nCores=1)
tppccrResults <- tppccrResultTable(data=tppccrFitted)
subset(tppccrResults, passed_filter_Panobinostat_1 & passed_filter_Panobinostat_2)