tpp2dSplineFitAndTest: Fit splines and perform f-Test

Description Usage Arguments Details Value Examples

View source: R/tpp2dSplineFitAndTest.R

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

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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

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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.