tpp2dSplineFitAndTest {TPP} | R Documentation

## Fit splines and perform f-Test

### Description

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

### Usage

    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
    )

### Arguments

`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

### Details

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.

### Value

None

### Examples

    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)

[Package TPP version 3.20.1 Index]