tests/testthat/prepare.R

In lujunyan1118/DrugScreenExplorer_dev: A pipeline for processing drug sensitivity screen data

#prepare expected data for unit testing

# Unit test for readScreen function
screenData <- readScreen(rawDir =  "testData/rawData/",
                         plateAnnotationFile = "testData/plateAnno/plateAnno.csv",
                         wellAnnotationFile = "testData/wellAnno/wellAnno.csv",
                         rowRange = c(3,18), colRange = 2,
                         sep = "[;\t]",
                         negWell <- c("DMSO","PBS"), posWell = c())


screenData_norm <- readScreen(rawDir =  "testData/rawData/",
                              plateAnnotationFile = "testData/plateAnno/plateAnno.csv",
                              wellAnnotationFile = "testData/wellAnno/wellAnno.csv",
                              rowRange = c(3,18), colRange = 2,
                              sep = "[;\t]",
                              negWell <- c("DMSO","PBS"), posWell = c(),
                              normalization = TRUE, method = "negatives")

screenData_norm_discard <- readScreen(rawDir =  "testData/rawData/",
                                      plateAnnotationFile = "testData/plateAnno/plateAnno.csv",
                                      wellAnnotationFile = "testData/wellAnno/wellAnno.csv",
                                      rowRange = c(3,18), colRange = 2,
                                      sep = "[;\t]",
                                      negWell <- c("DMSO","PBS"), posWell = c(),
                                      normalization = TRUE, method = "negatives", discardLayer = 2)

save(screenData, screenData_norm, screenData_norm_discard, file = "testData/expectedOutput/screenData.RData")


#Unit test for fitting edge effect
#load("tests/testthat/testData/expectedOutput/screenData.RData")

edgeFactor_loess <- fitEdgeEffect(screenData_norm, method = "loess",useNeg = TRUE, useLowConcentrations = 0)$edgeFactor
edgeFactor_loess_allWell <- fitEdgeEffect(screenData_norm, method = "loess",useNeg = FALSE, useLowConcentrations = 0)$edgeFactor
edgeFactor_sigmoid <- fitEdgeEffect(screenData_norm, method = "sigmoid",useNeg = TRUE, useLowConcentrations = 0)$edgeFactor
edgeFactor_sigmoid_allWell <- fitEdgeEffect(screenData_norm, method = "sigmoid",useNeg = FALSE, useLowConcentrations = 0)$edgeFactor

screenOnePlate <- dplyr::filter(screenData_norm, fileName == "P0010_11PB0010")
edgeVal1 <- estimateOnePlate(screenOnePlate, nLayer =1, onlyNeg = FALSE)
edgeVal2 <- estimateOnePlate(screenOnePlate, nLayer = 2, onlyNeg = TRUE)

save(edgeFactor_loess, edgeFactor_loess_allWell, edgeFactor_sigmoid,
     edgeFactor_sigmoid_allWell, screenOnePlate, edgeVal1, edgeVal2,
     file = "testData/expectedOutput/edgeFactor.RData")

# Unit test for correcting and estimate edge effect
screenData_edgeEstimated <- fitEdgeEffect(screenData_norm, method = "loess",useNeg = TRUE, useLowConcentrations = 0)
edgeCorr_bliss <- correctEdgeEffect(screenData_edgeEstimated, correctMethod = "bliss")
edgeCorr_linear <- correctEdgeEffect(screenData_edgeEstimated, correctMethod = "linear")
save(screenData_edgeEstimated, edgeCorr_bliss, edgeCorr_linear, file = "testData/expectedOutput/edgeCorrected.RData")


# Unit tests for summarizing screen data
screenSub <- dplyr::filter(screenData_norm, patientID %in% c("P0010","P0007"))
sumData_average <- summariseScreen(screenSub, method = "average")
sumData_AUC <- summariseScreen(screenSub, method = "AUC")
screenSub_edgeCorr <- correctEdgeEffect(screenSub)
sumData_AUC_corr <- summariseScreen(screenSub_edgeCorr, method = "AUC")
sumData_IC50 <- summariseScreen(screenSub_edgeCorr, method = "IC50")

tabDose1 <- dplyr::filter(screenData_norm, sampleID == "11PB0010", name == "Venetoclax")
tabDose2 <- dplyr::filter(screenData_norm, sampleID == "11PB0010", name == "Ibrutinib")
fitRes1 <- sumIC50(normVal ~ concentration, tabDose1)
fitRes2 <- sumIC50(normVal ~ concentration, tabDose2)
save(screenSub, sumData_average, sumData_AUC, screenSub_edgeCorr, sumData_AUC_corr, sumData_IC50,
     tabDose1, tabDose2, fitRes1, fitRes2, file = "testData/expectedOutput/summarisedData.RData")