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

Description Usage Arguments Value Examples

View source: R/tpp2dCurveFit.R

Description

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

Usage

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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

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# 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)
  

Bioconductor-mirror/TPP documentation built on July 7, 2017, 11:01 p.m.