tpp2dMerge2dRef: Merge 2D-TPP result data with TPP-TR reference data

Description Usage Arguments Details Value See Also Examples

View source: R/tpp2dMerge2dRef.R

Description

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

Usage

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

Arguments

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

Details

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.

Value

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

See Also

tpp2dCreateTPPTRreference

Examples

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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)

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