## ----style, eval=TRUE, echo=FALSE, results='asis'------------------------
BiocStyle::latex()


## ----opts, include=FALSE-------------------------------------------------
knitr::opts_chunk$set(concordance=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, eval=TRUE--------------------------------------------------
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", "Replicate")],
           "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, eval=TRUE, cache=TRUE------------------------------------
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
TRresultsBNew <- tpptrResultTable(data=trDataFitted, binWidth=bNew)


## ----compBWidth----------------------------------------------------------
tr_targetsBNew <- subset(TRresultsBNew, fulfills_all_4_requirements==TRUE)$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, eval=TRUE, cache=TRUE-----------------------------------
CCRresults <- analyzeTPPCCR(configTable=hdacCCR_config_repl1, data=hdacCCR_data_repl1,
                            resultPath=resultPath, plotCurves=FALSE) 


## ----ccrTargets----------------------------------------------------------
ccr_targets <- subset(CCRresults, passed_filter)$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_repl1, data=hdacCCR_data_repl1)


## ----ccrNormalization, message=TRUE--------------------------------------
ccrDataNormalized <- tppccrNormalize(data=ccrData)


## ----ccrTransform, message=TRUE------------------------------------------
ccrDataTransformed <- tppccrTransform(data=ccrDataNormalized)


## ----ccrSelectHDACs------------------------------------------------------
ccrDataHDAC <- ccrDataTransformed[match(hdac_targets, featureNames(ccrDataTransformed)),]


## ----ccrFitHDAC, message=TRUE--------------------------------------------
ccrResultsHDAC <- tppccrCurveFit(data=ccrDataHDAC, resultPath=resultPath)


## ----fittedDRPars--------------------------------------------------------
print(ccrResultsHDAC[,c(1, 12:15)])