R: Run TPP-CCR analysis for 2D-TPP experiment

tpp2dCurveFit {TPP}

R Documentation

Run TPP-CCR analysis for 2D-TPP experiment

Description

Performs analysis of a TPP-CCR experiment by invoking the routine for TPP-CCR curve fitting for each temperature of the sample.

Usage

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)

Arguments

`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.

Value

A data frames in which the fit results are stored row-wise for each protein.

Examples

# 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)

[Package TPP version 3.15.3 Index]