tpptrCurveFit: Fit melting curves to all proteins in a dataset.

In DoroChilds/TPP: Analyze thermal proteome profiling (TPP) experiments

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 ExpressionSets with protein fold changes for curve fitting.
dataCI	list of ExpressionSets 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"]]))

DoroChilds/TPP documentation built on Oct. 31, 2021, 4:38 a.m.