tppccrCurveFit {TPP} | R Documentation

## Fit dose response curves

### Description

`tppccrCurveFit` fits logistic dose response curves to fold change measurements of a TPP-CCR experiment.

### Usage

    tppccrCurveFit(
      data = NULL,
      fcTable = NULL,
      cpdEffects = NULL,
      slopeBounds = c(1, 50),
      nCores = "max",
      verbose = FALSE
    )

### Arguments

`data` | list of expressionSet objects containing protein fold changes for dose response curve fitting.
`fcTable` | optional long table with fold changes for each experiment. Can be provided instead of the input argument `data`.
`cpdEffects` | optional long table of compound effects per protein and experiment. Can be provided instead of the input argument `data`.
`slopeBounds` | bounds on the slope parameter for dose response curve fitting.
`nCores` | either a numerical value given the desired number of CPUs, or 'max' to automatically assign the maximum possible number (default).
`verbose` | print name of each fitted protein to the command line as a means of progress report.

### Details

`data` is a list of expressionSet objects created by `tppccrImport`. If desired, it can be already preprocessed by `tppccrNormalize` or `tppccrTransform`. It contains the isobaric labels and administered drug concentrations in the `phenoData` and user-defined protein properties in the `featureData`. Protein IDs are stored in the `featureNames`.

Measurements and compound effects for curve fitting can be provided by the arguments `fcTable` and `cpdEffects`, instead of being stored in expressionSets in `data`.

If specified, `fcTable` needs to be a long table with column names "id" (the protein names), "concentration" (the fold changes), "labelName" (the isobaric label to each measurement), and "experiment" (e.g. "Vehicle_1" or "Panobinostat_1").

If specified, `cpdEffects` needs to be a long table with column names "id" (the protein names), "cpdEff" (character vector of compound effects, may contain NAs), and "experiment" (e.g. "Vehicle_1" or "Panobinostat_1").

### Value

A list of expressionSet objects storing fold changes, the fitted curve parameters, as well as row and column metadata. In each expressionSet `S`, the fold changes can be accessed by `Biobase::exprs(S)`. Protein expNames can be accessed by `featureNames(S)`. Isobaric labels and the corresponding concentrations are returned by `S$label` and `S$concentration`. The fitted curve parameters are stored in codefeatureData(S).

### See Also

`tppccrImport`, `tppccrNormalize`, `tppccrTransform`

### Examples

    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)

[Package TPP version 3.20.1 Index]