tpp2dSplinePlot: Fit splines and generate ggplot visualizations

In 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

tpp2dSplinePlot(
  data_2D = NULL,
  trRef = NULL,
  fcStr = NULL,
  idVar = NULL,
  refIdVar = "Protein_ID",
  methods = c("doseResponse", "splineFit"),
  refFcStr = "norm_rel_fc_protein_",
  verbose = FALSE
)

Arguments

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 fcStr will be pasted in front of the names of the experiments.
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

Value

A list of ggplots which can be accessed via the unique protein ids in the idVar column

Examples

load(system.file("example_data/2D_example_data/shortData2d.RData", package="TPP"))
trRef <- system.file("example_data/2D_example_data/referenceNormData.RData", package="TPP")

TPP documentation built on Nov. 8, 2020, 5:55 p.m.