tpp2dSplinePlot {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
tpp2dSplinePlot( data_2D = NULL, trRef = NULL, fcStr = NULL, idVar = NULL, refIdVar = "Protein_ID", methods = c("doseResponse", "splineFit"), refFcStr = "norm_rel_fc_protein_", verbose = FALSE )
data_2D |
result data.frame from a 2D-TPP CCR analysis |
trRef |
character string of a valid system path to a TPP-TR reference RData object |
fcStr |
character string indicating how columns that will contain the actual
fold change values will be called. The suffix |
idVar |
character string indicating name of the columns containing the unique protein identifiers in the 2D data set |
refIdVar |
character string indicating name of the columns containing the unique protein identifiers in the reference data set |
methods |
vector of character strings that indicate which methods has been used for the previous analysis (default: c("doseResponse"), alternative: c("splineFit") or c("doseResponse", "splineFit")) |
refFcStr |
character string indicating how columns that will contain the fold change values in the reference data set |
verbose |
print description of problems for each protein for which splines fits could not be performed |
A list of ggplots which can be accessed via the unique protein ids in the idVar column
load(system.file("example_data/2D_example_data/shortData2d.RData", package="TPP")) trRef <- system.file("example_data/2D_example_data/referenceNormData.RData", package="TPP")