tests/testthat/test-compute.R
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 data("count_table", package = "ScreenR")
 data("annotation_table", package = "ScreenR")
 data <- count_table
 annotaion <- annotation_table
 
 groups <- factor(c(
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     "T1/T2", "T1/T2", "Treated", "Treated", "Treated",
     "Control", "Control", "Control", "Treated", "Treated", "Treated",
     "Control", "Control", "Control"
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 ))
 
 
 palette <- c(
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     "#1B9E75", "#1B9E75", "#D95F02", "#D95F02", "#D95F02",
     "#7570B3", "#7570B3", "#7570B3", "#E7298A", "#E7298A", "#E7298A",
     "#66A61E", "#66A61E", "#66A61E"
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 )
 
 create_test_object <- function() {
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     data <- data %>%
         dplyr::filter(Barcode != "*")
 
     colnames(data) <- c(
         "Barcode", "T1", "T2", "Time3_TRT_A", "Time3_TRT_B", "Time3_TRT_C",
         "Time3_A", "Time3_B", "Time3_C", "Time4_TRT_A", "Time4_TRT_B",
         "Time4_TRT_C", "Time4_A", "Time4_B", "Time4_c"
     )
     obj <- create_screenr_object(
         table = data,
         annotation = annotaion, groups = groups, replicates = c("")
     )
     obj <- normalize_data(obj)
     obj <- compute_data_table(obj)
 
     obj@data_table <- obj@data_table %>%
         dplyr::filter(Gene %in% paste0("Gene_", seq(1, 10)))
 
     obj@normalized_count_table <- obj@normalized_count_table %>%
         dplyr::filter(Barcode %in% obj@data_table$Barcode)
 
     obj@count_table <- obj@count_table %>%
         dplyr::filter(Barcode %in% obj@data_table$Barcode)
 
     obj@annotation_table <- obj@annotation_table %>%
         dplyr::filter(Barcode %in% obj@data_table$Barcode)
 
     return(obj)
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 }
 
 test_that("Compute Metrics ", {
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     object <- create_test_object()
 
     # In order to speed up the test we will compute the metrics only for a
     # subset of the genes
     genes <- c("Gene_1", "Gene_5")
     object@data_table <- object@data_table[object@data_table$Gene %in% genes, ]
     table <- compute_metrics(object,
         treatment = "TRT", control = "Time3",
         day = "Time3"
     )
     expect_equal(class(table)[1], "tbl_df")
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 })
 
 test_that("Camera", {
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     object <- create_test_object()
 
     matrix <- model.matrix(~ object@groups)
     colnames(matrix) <- c("Control", "T1/T2", "Treated")
     camera_hit <- suppressWarnings(find_camera_hit(
         screenR_Object = object,
         matrix_model = matrix, contrast = "Treated"
     ))
     expect_equal(class(camera_hit)[1], "tbl_df")
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 })
 
 
 
 test_that("Number of Barcode Lost", {
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     library(tibble)
 
     object <- create_screenr_object(
         table = data,
         annotation = annotaion, groups = groups, replicates = c("")
     )
     barcode_lost <- barcode_lost(object)
     expect_equal(is_tibble(barcode_lost), TRUE)
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 })
 
 
 test_that("Create data_table", {
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     object <- create_screenr_object(
         table = data,
         annotation = annotaion, groups = groups, replicates = c("")
     )
     object <- normalize_data(object)
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     object <- compute_data_table(object)
     expect_equal(class(object@data_table)[1], "tbl_df")
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 })
 
 
 test_that("Normalize Data", {
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     object <- create_screenr_object(
         table = data,
         annotation = annotaion, groups = groups, replicates = c("")
     )
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     object <- normalize_data(object)
     expect_equal(dim(object@count_table), dim(object@normalized_count_table))
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 })
 
 test_that("Number mapped reads", {
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     library(tibble)
     object <- create_screenr_object(
         table = data,
         annotation = annotaion, groups = groups, replicates = c("")
     )
     mapped <- mapped_reads(object)
 
     expect_equal(is_tibble(mapped), TRUE)
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 })