tpp2dSplinePlot: Fit splines and generate ggplot visualizations

Description Usage Arguments Value Examples

View source: R/tpp2dSplinePlot.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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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

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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.