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 3.16.5 Index]