tpp2dCurveFit {TPP} | R Documentation |
Performs analysis of a TPP-CCR experiment by invoking the routine for TPP-CCR curve fitting for each temperature of the sample.
tpp2dCurveFit( configFile = NULL, data, nCores = 1, naStrs = NULL, fcStr = NULL, idVar = NULL, nonZeroCols = NULL, r2Cutoff = 0.8, fcCutoff = 1.5, slopeBounds = c(1, 50), fcTolerance = 0.1 )
configFile |
DEPCRECATED |
data |
data frame that contains the data of the 2D-TPP experiment for each temperature. |
nCores |
numeric value stating how many cores are to be used for computation |
naStrs |
DEPCRECATED |
fcStr |
DEPCRECATED |
idVar |
DEPCRECATED |
nonZeroCols |
DEPCRECATED |
r2Cutoff |
Quality criterion on dose response curve fit. |
fcCutoff |
Cutoff for highest compound concentration fold change. |
slopeBounds |
Bounds on the slope parameter for dose response curve fitting. |
fcTolerance |
tolerance for the fcCutoff parameter. See details. |
A data frames in which the fit results are stored row-wise for each protein.
# Preparation: data(panobinostat_2DTPP_smallExample) # Import data: datIn <- tpp2dImport(configTable = panobinostat_2DTPP_config, data = panobinostat_2DTPP_data, idVar = "representative", addCol = "clustername", intensityStr = "sumionarea_protein_", nonZeroCols = "qusm") # Compute fold changes: datFC <- tpp2dComputeFoldChanges(data = datIn) # Perform median normalization: datNorm <- tpp2dNormalize(data = datFC) # View updated attributes. Now contain field 'fcStrNorm' indicating prefix # of the fold change columns after normalization. attr(datNorm, "importSettings")["fcStrNorm"] # Perform dose response curve fitting and pEC50 calculation: datFit <- tpp2dCurveFit(data = datNorm)