tpp2dSplineFitAndTest: Fit splines and perform f-Test
In TPP: Analyze thermal proteome profiling (TPP) experiments

Description Usage Arguments Details Value Examples

Fit splines through TR reference dataset and extrapolates relative 2D-TPP datapoints, then compares spline fits of different treatments with non-treatment with an f-test

tpp2dSplineFitAndTest(
  data_2D = NULL,
  data,
  trRefDataPath = NULL,
  dataRef,
  refIDVar = "Protein_ID",
  refFcStr = "norm_rel_fc_",
  resultPath = NULL,
  doPlot = TRUE,
  verbose = FALSE,
  nCores = "max",
  ggplotTheme = NULL
)

`data_2D`	DEPRECATED
`data`	result data.frame from a 2D-TPP CCR analysis
`trRefDataPath`	DEPRECATED
`dataRef`	reference data from a TPP TR analysis on the same cell line as
`refIDVar`	character string indicating name of the columns containing the unique protein identifiers in the reference data set
`refFcStr`	character string indicating which columns contain the actual fold change values in the reference data. The suffix `fcStr` will be pasted in front of the names of the experiments.
`resultPath`	location where to store dose-response curve plots and results table.
`doPlot`	boolean value indicating whether protein-wise plots should be produced Deactivating plotting decreases runtime.
`verbose`	print description of problems for each protein for which splines fits could not be performed
`nCores`	either a numerical value given the desired number of CPUs, or 'max' to automatically assign the maximum possible number (default).
`ggplotTheme`	DEPRECATED

dataRef can either be a tidy data frame of TPP-TR reference data, a list with TPP-TR reference data and additional information produced by tpp2dCreateTPPTRreference, or a character string with a link to the data in one of the described formats.

None

data(panobinostat_2DTPP_smallExample)
config_tpp2d <- panobinostat_2DTPP_config
data_tpp2d <- panobinostat_2DTPP_data
trRef <- file.path(system.file("data", package="TPP"), 
  "TPPTR_reference_results_HepG2.RData")
datIn <- tpp2dImport(configTable = config_tpp2d,
                      data = data_tpp2d,
                      idVar = "representative",
                      addCol = "clustername",
                      intensityStr = "sumionarea_protein_",
                      nonZeroCols = "qusm")
fcData2d <- tpp2dComputeFoldChanges(data = datIn)
normData2d <- tpp2dNormalize(data = fcData2d)
analysisResults <- tpp2dSplineFitAndTest(data = normData2d,
                                         dataRef = trRef,
                                         refIDVar = "Protein_ID",
                                         refFcStr = "norm_rel_fc_protein_",
                                         doPlot = FALSE,
                                         nCores = 1)