tpptrCurveFit {TPP} | R Documentation

## Fit melting curves to all proteins in a dataset.

### Description

Fit melting curves to all proteins in a dataset.

### Usage

    tpptrCurveFit(
      data,
      dataCI = NULL,
      resultPath = NULL,
      ggplotTheme = tppDefaultTheme(),
      doPlot = TRUE,
      startPars = c(Pl = 0, a = 550, b = 10),
      maxAttempts = 500,
      nCores = "max",
      verbose = FALSE
    )

### Arguments

`data` | list of `ExpressionSet`s with protein fold changes for curve fitting.
`dataCI` | list of `ExpressionSet`s with protein fold change confidence intervals for curve fitting. Default to NULL.
`resultPath` | location where to store the melting curve plots.
`ggplotTheme` | ggplot theme for melting curve plots.
`doPlot` | boolean value indicating whether melting curves should be plotted, or whether just the curve parameters should be returned.
`startPars` | start values for the melting curve parameters. Will be passed to function `nls` for curve fitting.
`maxAttempts` | maximal number of curve fitting attempts if model does not converge.
`nCores` | either a numerical value given the desired number of CPUs, or 'max' to automatically assign the maximum possible number (default).
`verbose` | plot name of each fitted protein to the command lin as a means of progress report.

### Details

If the melting curve fitting procedure does not converge, it will be repeatedly started from perturbed starting parameters (maximum iterations defined by argument `maxAttempts`)

If `doPlot = TRUE`, melting curves are be plotted in individual files per protein. Each file is named by its unique identifier. Filenames are truncated to 255 characters (requirement by most operation systems). Truncated filenames are indicated by the suffix "_truncated[d]", where [d] is a unique number to avoid redundancies.

The melting curve plots will be stored in a subfolder with name `Melting_Curves` at the location specified by `resultPath`.

### Value

A list of ExpressionSets storing the data together with the melting curve parameters for each experiment. Each ExpressionSet contains the measured fold changes, 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 temperatures are returned by `S$label` and `S$temperature`.

### See Also

`tppDefaultTheme`

### Examples

    data(hdacTR_smallExample)
    tpptrData <- tpptrImport(configTable=hdacTR_config, data=hdacTR_data)
    tpptrNorm <- tpptrNormalize(data=tpptrData, normReqs=tpptrDefaultNormReqs())
    normalizedData <- tpptrNorm$normData
    hdacSubsets <- lapply(normalizedData,
                          function(d) d[grepl("HDAC", Biobase::featureNames(d))])
    tpptrFittedHDACs <- tpptrCurveFit(hdacSubsets, nCores=1)
    # Show estimated parameters for vehicle and treatment experiments:
    Biobase::pData(Biobase::featureData(tpptrFittedHDACs[["Vehicle_1"]]))
    Biobase::pData(Biobase::featureData(tpptrFittedHDACs[["Panobinostat_1"]]))

[Package TPP version 3.16.5 Index]