tpp2dMerge2dRef: Merge 2D-TPP result data with TPP-TR reference data
In DoroChilds/TPP: Analyze thermal proteome profiling (TPP) experiments

Description Usage Arguments Details Value See Also Examples

Merges 2D-TPP result data with TPP-TR reference data to generate a big table including both results

tpp2dMerge2dRef(
  resultTable_2D,
  referenceDataSummary,
  refIDVar = "Protein_ID",
  idVar = NULL,
  data = NULL,
  trRef = NULL
)

`resultTable_2D`	dataframe containing the 2D-TPP results
`referenceDataSummary`	summarized reference data results. See details.
`refIDVar`	character string indicating name of the columns containing the unique protein identifiers in the reference data set
`idVar`	DEPRECATED
`data`	DEPRECATED
`trRef`	DEPRECATED

referenceSummary contains summary statistics like median fold changes and is produced by the function tpp2dCreateTPPTRreference. It summarizes the results of a TPP-TR analysis of a reference data set. A reference data set is the a output of a TR experiment without drug treatment on the same cell line as resultTable_2D.

A data frame with results merged from 2D-TPP and TPP-TR reference

tpp2dCreateTPPTRreference

 
data(panobinostat_2DTPP_smallExample)
config_tpp2d <- panobinostat_2DTPP_config
data_tpp2d <- panobinostat_2DTPP_data
tpp2dResults <- analyze2DTPP(configTable = config_tpp2d, 
                             data = data_tpp2d,
                             methods=c("doseResponse"),
                             createReport="none",
                             nCores=1,
                             idVar = "representative",
                             addCol = "clustername",
                             intensityStr = "sumionarea_protein_",
                             nonZeroCols = "qusm") 

trRef <- file.path(system.file("data", package="TPP"), 
"TPPTR_reference_results_HepG2.RData")

annotatedTable <- tpp2dMerge2dRef(resultTable_2D = tpp2dResults,
                                  referenceDataSummary = trRef)