tpp2dCurveFit: Run TPP-CCR analysis for 2D-TPP experiment

In DoroChilds/TPP: Analyze thermal proteome profiling (TPP) experiments

Description

Performs analysis of a TPP-CCR experiment by invoking the routine for TPP-CCR curve fitting for each temperature of the sample.

Usage

tpp2dCurveFit(
  configFile = NULL,
  data,
  nCores = 1,
  naStrs = NULL,
  fcStr = NULL,
  idVar = NULL,
  nonZeroCols = NULL,
  r2Cutoff = 0.8,
  fcCutoff = 1.5,
  slopeBounds = c(1, 50),
  fcTolerance = 0.1
)

Arguments

configFile	DEPCRECATED
data	data frame that contains the data of the 2D-TPP experiment for each temperature.
nCores	numeric value stating how many cores are to be used for computation
naStrs	DEPCRECATED
fcStr	DEPCRECATED
idVar	DEPCRECATED
nonZeroCols	DEPCRECATED
r2Cutoff	Quality criterion on dose response curve fit.
fcCutoff	Cutoff for highest compound concentration fold change.
slopeBounds	Bounds on the slope parameter for dose response curve fitting.
fcTolerance	tolerance for the fcCutoff parameter. See details.

Value

A data frames in which the fit results are stored row-wise for each protein.

Examples

# Preparation:
data(panobinostat_2DTPP_smallExample)

# Import data:
datIn <- tpp2dImport(configTable = panobinostat_2DTPP_config,
                      data = panobinostat_2DTPP_data,
                      idVar = "representative",
                      addCol = "clustername",
                      intensityStr = "sumionarea_protein_",
                      nonZeroCols = "qusm")

# Compute fold changes:
datFC <- tpp2dComputeFoldChanges(data = datIn)

# Perform median normalization:
datNorm <- tpp2dNormalize(data = datFC)

# View updated attributes. Now contain field 'fcStrNorm' indicating prefix
# of the fold change columns after normalization.
attr(datNorm, "importSettings")["fcStrNorm"]

# Perform dose response curve fitting and pEC50 calculation:
datFit <- tpp2dCurveFit(data = datNorm)
  

DoroChilds/TPP documentation built on Oct. 31, 2021, 4:38 a.m.