tpp2dSplineFitAndTest: Fit splines and perform f-Test

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

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)
  

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