## ----style-knitr, eval=TRUE, echo=FALSE, results='asis'-------------------- BiocStyle::latex() ## ----opts, include=FALSE, echo=FALSE--------------------------------------- knitr::opts_chunk$set(concordance = TRUE, eval = TRUE, cache = FALSE, resize.width="0.45\\textwidth", fig.align='center', tidy = FALSE, message=FALSE, warning = FALSE) ## ----install, eval=FALSE--------------------------------------------------- # if (!requireNamespace("BiocManager", quietly=TRUE)){ # install.packages("BiocManager") # } # BiocManager::install("TPP") ## ----package--------------------------------------------------------------- library("TPP") ## ----load_2d_data---------------------------------------------------------- data(panobinostat_2DTPP_smallExample, package = "TPP") ## ----head_2d_data, eval=TRUE----------------------------------------------- config_tpp2d <- panobinostat_2DTPP_config data_tpp2d <- panobinostat_2DTPP_data config_tpp2d data_tpp2d %>% str(1) ## ----colnames_Pano, eval=TRUE---------------------------------------------- data_tpp2d$X020466 %>% colnames ## ----ttp2dworkflow, eval = TRUE, warning=FALSE----------------------------- tpp2dResults <- analyze2DTPP(configTable = config_tpp2d, data = data_tpp2d, compFc = TRUE, idVar = "representative", intensityStr = "sumionarea_protein_", nonZeroCols = "qusm", addCol = "clustername", methods = "doseResponse", createReport = "none") tpp2dResults %>% mutate_if(is.character, factor) %>% summary ## ----ttp2dDataImport2, eval=TRUE, warning=FALSE---------------------------- data2d <- tpp2dImport(configTable = config_tpp2d, data = data_tpp2d, idVar = "representative", intensityStr = "sumionarea_protein_", nonZeroCols = "qusm", addCol = "clustername") head(data2d) attr(data2d, "importSettings") ## ----ttp2dComputeFC2, eval=TRUE-------------------------------------------- fcData2d <- tpp2dComputeFoldChanges(data = data2d) ## ----head_fold_changes2, eval=TRUE----------------------------------------- head(fcData2d) ## ----ttp2dDoMedianNorm2, eval=TRUE----------------------------------------- normData2d <- tpp2dNormalize(data = fcData2d) head(normData2d) ## ----tpp2dRunTPPCCR2, eval=TRUE, warning=FALSE----------------------------- ccr2dResults <- tpp2dCurveFit(data = normData2d) ## ----tpp2dPlotGoodCurves, eval=TRUE, warning=FALSE------------------------- drPlots <- tpp2dCreateDRplots(data = ccr2dResults, type = "good") ## ----plotCurve2, eval=TRUE, fig.height=6, fig.width=7.5-------------------- # Find IPI id for HDAC2 (in column representative): IPI_id_HDAC2 <- unique(filter(ccr2dResults, clustername == "HDAC2")$representative) # Show corresponding plot: drPlots[[IPI_id_HDAC2]] ## ----plotSingleCurves, eval=TRUE, fig.show='hide', fig.height=6, fig.width=7.5---- drPlotsByTemperature <- tpp2dCreateDRplots(data = ccr2dResults, type = "single") drPlotsByTemperature[[IPI_id_HDAC2]][["54"]] ## ----result_path_2DTPP, eval = TRUE---------------------------------------- resultPath = file.path(getwd(), 'Panobinostat_Vignette_Example_2D') if (!file.exists(resultPath)) dir.create(resultPath, recursive = TRUE) ## ----generateReferenceInputData, eval = FALSE, warning=FALSE--------------- # data("hdacTR_smallExample") # trConfig <- hdacTR_config[1:2,] %>% # dplyr::select(-dplyr::matches("Comparison")) # # trConfig ## ----generateReferenceOject, eval = FALSE, warning=FALSE------------------- # tpp2dCreateTPPTRreference(trConfigTable = trConfig, # trDat = hdacTR_data[1:2], # resultPath = resultPath, # outputName = "desired_file_name", # createFCboxplots = FALSE) ## ----pE50plots, eval = TRUE, warning = FALSE------------------------------- # set the system path for the HepG2 TR reference data set: trRef <- file.path(system.file("data", package="TPP"), "TPPTR_reference_results_HepG2.RData") plotData <- ccr2dResults %>% filter(clustername == "HDAC2") pEC50QC_HDAC1 <- tpp2dPlotQCpEC50(resultTable = plotData, resultPath = NULL, trRef = trRef, idVar = "representative") pEC50QC_HDAC1[[1]] ## ----qcHists, eval = FALSE, warning=FALSE---------------------------------- # tpp2dPlotQChist(configFile = config_tpp2d, # resultTable = ccr2dResults, # resultPath = resultPath, # trRef = trRef, # idVar = "representative")