tppccrCurveFit: Fit dose response curves
In TPP: Analyze thermal proteome profiling (TPP) experiments

Description Usage Arguments Details Value See Also Examples

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

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

`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.

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").

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).

tppccrImport, tppccrNormalize, tppccrTransform

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)