## ----style, echo=FALSE, results='asis'----------------------------------- BiocStyle::latex() ## ----opts, include=FALSE------------------------------------------------- knitr::opts_chunk$set(concordance=TRUE, eval = TRUE, cache = TRUE, resize.width="0.45\\textwidth", fig.align='center', tidy = FALSE, message=FALSE) ## ----install, eval=FALSE------------------------------------------------- ## source("http://bioconductor.org/biocLite.R") ## biocLite("TPP") ## ----package------------------------------------------------------------- library("TPP") ## ----load_tr_data-------------------------------------------------------- data("hdacTR_smallExample") ## ----locate_example_data------------------------------------------------- system.file('example_data', package = 'TPP') ## ----tr_config_table----------------------------------------------------- print(hdacTR_config) ## ----dataSummaryTP------------------------------------------------------- summary(hdacTR_data) ## ----dataStatsTP--------------------------------------------------------- data.frame(hdacTR_config[, c("Experiment", "Condition")], "No.of Proteins"=sapply(hdacTR_data, nrow), row.names=NULL) ## ----datahead------------------------------------------------------------ hdacVehicle1 <- hdacTR_data[["Vehicle_1"]] head(hdacVehicle1) ## ----result_path_TR------------------------------------------------------ resultPath = file.path(getwd(), 'Panobinostat_Vignette_Example') ## ----analyzeTR----------------------------------------------------------- TRresults <- analyzeTPPTR(configTable=hdacTR_config, data=hdacTR_data, nCores=2, resultPath=resultPath, plotCurves=FALSE) ## ----trTargets----------------------------------------------------------- tr_targets <- subset(TRresults, fulfills_all_4_requirements)$Protein_ID print(tr_targets) ## ----trHDACTargets------------------------------------------------------- hdac_targets <- grep("HDAC", tr_targets, value=TRUE) print(hdac_targets) ## ----trImport, message=TRUE---------------------------------------------- trData <- tpptrImport(configTable=hdacTR_config, data=hdacTR_data) ## ----trData_vehicle1----------------------------------------------------- trData[["Vehicle_1"]] ## ----trDefaultNormReqs--------------------------------------------------- print(tpptrDefaultNormReqs()) ## ----trNormalization, message=TRUE--------------------------------------- normResults <- tpptrNormalize(data=trData) trDataNormalized <- normResults[["normData"]] ## ----trSelectHDACs------------------------------------------------------- trDataHDAC <- lapply(trDataNormalized, function(d) d[featureNames(d) %in% hdac_targets,]) ## ----trFitHDAC, message=TRUE--------------------------------------------- trDataHDAC <- tpptrCurveFit(data=trDataHDAC, resultPath=resultPath, nCores=1) ## ----fittedMeltPars------------------------------------------------------ pData(featureData(trDataHDAC[["Vehicle_1"]]))[,1:5] ## ----loadTRfitResultss--------------------------------------------------- load(file.path(resultPath, "dataObj", "fittedData.RData"), verbose=TRUE) ## ----trPvals, message=TRUE----------------------------------------------- bNew <- 200 print(sapply(trDataFitted, annotation)) TRresultsBNew <- tpptrAnalyzeMeltingCurves(data=trDataFitted, pValParams=list(binWidth=bNew, minR2=0.8, maxPlateau=0.3)) ## ----compBWidth---------------------------------------------------------- tr_targetsBNew <- subset(TRresultsBNew, fulfills_all_4_requirements)$Protein_ID onlyB300 <- setdiff(tr_targets, tr_targetsBNew) onlyBNew <- setdiff(tr_targetsBNew, tr_targets) print(onlyB300) print(onlyBNew) ## ----trExport, message=TRUE---------------------------------------------- tppExport(tab=TRresultsBNew, file=file.path(resultPath, paste("targets_binWidth",bNew,".xlsx",sep=""))) ## ----newNormReqs--------------------------------------------------------- trNewReqs <- tpptrDefaultNormReqs() print(trNewReqs) trNewReqs$otherRequirements[1,"colName"] <- "mycolName" trNewReqs$fcRequirements[,"fcColumn"] <- c(6,8,9) print(trNewReqs) ## ----load_ccr_data------------------------------------------------------- data("hdacCCR_smallExample") ## ----analyzeCCR---------------------------------------------------------- CCRresults <- analyzeTPPCCR(configTable=hdacCCR_config[1,], data=hdacCCR_data[[1]], resultPath=resultPath, plotCurves=FALSE, nCores=1) ## ----ccrTargets---------------------------------------------------------- ccr_targets <- subset(CCRresults, passed_filter_Panobinostat_1)$Protein_ID print(ccr_targets) ## ----ccrHDACTargets------------------------------------------------------ hdac_targets <- grep("HDAC", ccr_targets, value=TRUE) print(hdac_targets) ## ----ccrImport, message=TRUE--------------------------------------------- ccrData <- tppccrImport(configTable=hdacCCR_config[1,], data=hdacCCR_data[[1]]) ## ----ccrNormalization, message=TRUE-------------------------------------- ccrDataNormalized <- tppccrNormalize(data=ccrData) ## ----ccrTransform, message=TRUE------------------------------------------ ccrDataTransformed <- tppccrTransform(data=ccrDataNormalized)[[1]] ## ----ccrSelectHDACs------------------------------------------------------ ccrDataHDAC <- ccrDataTransformed[match(hdac_targets, featureNames(ccrDataTransformed)),] ## ----ccrFitHDAC, message=TRUE-------------------------------------------- ccrDataFittedHDAC <- tppccrCurveFit(data=list(Panobinostat_1=ccrDataHDAC), nCores=1) tppccrPlotCurves(ccrDataFittedHDAC, resultPath=resultPath, nCores=1) ## ----fittedDRPars-------------------------------------------------------- ccrResultsHDAC <- tppccrResultTable(ccrDataFittedHDAC) print(ccrResultsHDAC[,c(1, 22:25)])