tpp2dSplineFitAndTest {TPP} | R Documentation |
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 |
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)