tpp2dExport: Produce Excel table of 2D-TPP experiment.

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

Description

Produce Excel table of 2D-TPP experiment analysis results.

Usage

tpp2dExport(
  configTable = NULL,
  tab,
  resultPath = NULL,
  idVar = NULL,
  fcStr = NULL,
  intensityStr = NULL,
  outPath,
  addCol = NULL,
  normalizedData = NULL,
  trRef = NULL,
  addPlotColumns = TRUE
)

Arguments

configTable	DEPRECATED
tab	Table with results of the 2D-TPP analysis.
resultPath	DEPRECATED
idVar	DEPRECATED
fcStr	DEPRECATED
intensityStr	DEPRECATED
outPath	path for storing results table
addCol	additional names of columns which are to be attached to the result table
normalizedData	DEPRECATED
trRef	character string containing a valid system path to a TPP-TR reference RData file
addPlotColumns	boolean variable indicating whether paths to plot files should be generated and checked for validity. De-activate if no dose-response curve plots were produced during the analysis.

Value

Creates excel file of the TPP-CCR analysis of the 2D-TPP data.

Examples

data(panobinostat_2DTPP_smallExample)
load(system.file("example_data/2D_example_data/shortData2d.RData", package="TPP"))
# tpp2dExport(configTable = panobinostat_2DTPP_config, tab=shortData2d, 
#             outPath=getwd(), 
#             idVar="representative", fcStr="norm_rel_fc_protein_", 
#             intensityStr="sumionarea_protein_", addCol=NULL)

data(panobinostat_2DTPP_smallExample)
# cfgRaw <- panobinostat_2DTPP_config
# datRaw <- panobinostat_2DTPP_data
# datIn <- tpp2dImport(cfgIn, datRaw, fcStr = NULL)
# datFC <- tpp2dComputeFoldChanges(data = datIn)
# datNorm <- tpp2dNormalize(data = datFC)
# cfgCCR <- convert_2D_cfgTable_to_CCR_cfgTable(cfgIn)
# datFitted <- tpp2dCurveFit(datNorm, nCores = 2)
# tpp2dCreateReport(getwd(), cfgIn, resultTable = datFitted, idVar = "representative", 
#                   intensityStr = "sumionarea_protein_")
# tpp2dExport(tab = datFitted, outPath = getwd(), addPlotColumns = FALSE) 

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