tests/testthat/test_normalizeData.R
In CancerRxGene/gdscIC50: Pipeline for GDSC Curve Fitting
context("Test calcTagMean")
test_that("calcTagMean", {
test_data <- rbind(
data.frame(SCAN_ID = 101, TAG = "NC1", INTENSITY = c(4648, 9846, 1563, 1519)),
data.frame(SCAN_ID = 101, TAG = "NC2", INTENSITY = c(4648, 9846, 1563, 1519)),
data.frame(SCAN_ID = 102, TAG = "NC2", INTENSITY = c(1672, 4366, 1651, 6527)),
data.frame(SCAN_ID = 103, TAG = "NC1", INTENSITY = c(6175, 1381, 4367, 6345)),
data.frame(SCAN_ID = 103, TAG = "NC2", INTENSITY = c(NA, NA, NA, NA))
)
# No tag at all of "foo"
expect_error(calcTagMean(test_data, "foo"),
"is not present for some or all of the SCAN_IDs in your data")
# No NC1 for scan 102
expect_error(calcTagMean(test_data, "NC1"),
"is not present for some or all of the SCAN_IDs in your data")
# Mean of NC2 for scan 103 is NaN
expect_error(calcTagMean(test_data, "NC2"),
"has a mean of NaN for some or all of the SCAN_IDs in your data")
})
context("Test normalize data")
test_that("normalizeData returns a data frame for single agent only data", {
# data("gdsc_example")
test_data <- readRDS("norm_single_agents_test.rds")
norm_data <- normalizeData(test_data,
neg_control = "NC-1",
pos_control = "PC1-D1-S")
expect_true(is.data.frame(norm_data))
expected_names <- c("SCAN_ID",
"BARCODE",
"RESEARCH_PROJECT",
"DATE_CREATED",
"DRUGSET_ID",
"CELL_LINE_NAME",
"CELL_ID",
"MASTER_CELL_ID",
"COSMIC_ID",
"POSITION",
"DRUG_ID_lib",
"CONC",
"INTENSITY",
"lib_drug",
"dose",
"treatment",
"NC",
"PC",
"normalized_intensity",
"norm_neg_pos",
"time_stamp",
"sw_version")
expect_named(norm_data, expected_names)
})
test_that("normalizeData returns a data frame with combination treatment
data with the right names", {
test_data <- readRDS("combo_norm_data_test.rds")
norm_data <- normalizeData(test_data,
neg_control = "NC-1",
pos_control = "B")
expect_true(is.data.frame(norm_data))
expected_names <- c("SCAN_ID",
"BARCODE",
"RESEARCH_PROJECT",
"DATE_CREATED",
"DRUGSET_ID",
"CELL_LINE_NAME",
"CELL_ID",
"MASTER_CELL_ID",
"COSMIC_ID",
"POSITION",
"DRUG_ID_lib",
"CONC",
"INTENSITY",
"lib_drug",
"dose",
"treatment",
"DRUG_ID_anch",
"CONC_anch",
"anchor",
"NC",
"PC",
"normalized_intensity",
"norm_neg_pos",
"time_stamp",
"sw_version")
expect_named(norm_data, expected_names)
})
test_that("normalizeData maintains data mappings to barcode", {
test_data <- readRDS("norm_single_agents_test.rds")
norm_data <- normalizeData(test_data)
expect_identical(unique(test_data[test_data$BARCODE == 1234, "RESEARCH_PROJECT"]),
unique(norm_data[norm_data$BARCODE == 1234, "RESEARCH_PROJECT"]))
expect_identical(unique(test_data[test_data$BARCODE == 1234, "SCAN_ID"]),
unique(norm_data[norm_data$BARCODE == 1234, "SCAN_ID"]))
expect_identical(unique(test_data[test_data$BARCODE == 1234, "COSMIC_ID"]),
unique(norm_data[norm_data$BARCODE == 1234, "COSMIC_ID"]))
expect_identical(unique(test_data[test_data$BARCODE == 1234, "CELL_LINE_NAME"]),
unique(norm_data[norm_data$BARCODE == 1234, "CELL_LINE_NAME"]))
expect_identical(unique(test_data[test_data$BARCODE == 1234, "CELL_ID"]),
unique(norm_data[norm_data$BARCODE == 1234, "CELL_ID"]))
expect_identical(unique(test_data[test_data$BARCODE == 1234, "MASTER_CELL_ID"]),
unique(norm_data[norm_data$BARCODE == 1234, "MASTER_CELL_ID"]))
expect_identical(unique(test_data[test_data$BARCODE == 1234, "DRUGSET_ID"]),
unique(norm_data[norm_data$BARCODE == 1234, "DRUGSET_ID"]))
expect_identical(unique(test_data[test_data$BARCODE == 5678, "RESEARCH_PROJECT"]),
unique(norm_data[norm_data$BARCODE == 5678, "RESEARCH_PROJECT"]))
expect_identical(unique(test_data[test_data$BARCODE == 5678, "SCAN_ID"]),
unique(norm_data[norm_data$BARCODE == 5678, "SCAN_ID"]))
expect_identical(unique(test_data[test_data$BARCODE == 5678, "COSMIC_ID"]),
unique(norm_data[norm_data$BARCODE == 5678, "COSMIC_ID"]))
expect_identical(unique(test_data[test_data$BARCODE == 5678, "CELL_LINE_NAME"]),
unique(norm_data[norm_data$BARCODE == 5678, "CELL_LINE_NAME"]))
expect_identical(unique(test_data[test_data$BARCODE == 5678, "CELL_ID"]),
unique(norm_data[norm_data$BARCODE == 5678, "CELL_ID"]))
expect_identical(unique(test_data[test_data$BARCODE == 5678, "MASTER_CELL_ID"]),
unique(norm_data[norm_data$BARCODE == 5678, "MASTER_CELL_ID"]))
expect_identical(unique(test_data[test_data$BARCODE == 5678, "DRUGSET_ID"]),
unique(norm_data[norm_data$BARCODE == 5678, "DRUGSET_ID"]))
intensity_test <- merge(
test_data[, c("SCAN_ID", "POSITION", "INTENSITY")],
norm_data[, c("SCAN_ID", "POSITION", "INTENSITY")],
by = c("SCAN_ID", "POSITION"))
expect_identical(intensity_test$INTENSITY.x, intensity_test$INTENSITY.y)
})
test_that("normalizeData calculates correct mean values for negative controls", {
test_data <- readRDS("norm_single_agents_test.rds")
norm_data <- normalizeData(test_data,
neg_control = "NC-1",
pos_control = "PC1-D1-S")
expect_length(unique(norm_data[norm_data$SCAN_ID == 1199, "NC"]), 1)
expect_equal(unique(norm_data[norm_data$SCAN_ID == 1199, "NC"]),
mean(test_data[test_data$SCAN_ID == 1199 & test_data$TAG == 'NC-1',
"INTENSITY"]
)
)
expect_length(unique(norm_data[norm_data$SCAN_ID == 1299, "NC"]), 1)
expect_equal(unique(norm_data[norm_data$SCAN_ID == 1299, "NC"]),
mean(test_data[test_data$SCAN_ID == 1299 & test_data$TAG == 'NC-1',
"INTENSITY"]
)
)
})
test_that("normalizeData calculates correct mean values for positive controls", {
test_data <- readRDS("norm_single_agents_test.rds")
# Test PCs with different values
norm_data <- normalizeData(test_data,
neg_control = "NC-1",
pos_control = "B")
expect_length(unique(norm_data[norm_data$SCAN_ID == 1199, "PC"]), 1)
expect_equal(unique(norm_data[norm_data$SCAN_ID == 1199, "PC"]),
mean(test_data[test_data$SCAN_ID == 1199 & test_data$TAG == 'B',
"INTENSITY"]
)
)
expect_length(unique(norm_data[norm_data$SCAN_ID == 1299, "PC"]), 1)
expect_equal(unique(norm_data[norm_data$SCAN_ID == 1299, "PC"]),
mean(test_data[test_data$SCAN_ID == 1299 & test_data$TAG == 'B',
"INTENSITY"]
)
)
})
test_that("normalizeData calculates the normalized intensity correctly",{
test_data <- readRDS("norm_single_agents_test.rds")
norm_data <- normalizeData(test_data,
neg_control = "NC-1",
pos_control = "PC1-D1-S",
trim = "F")
normalization_test <- (norm_data$INTENSITY - norm_data$PC) / (norm_data$NC - norm_data$PC)
expect_identical(normalization_test, norm_data$normalized_intensity)
})
test_that("normalizeData trims the normalized intensity correctly",{
test_data <- readRDS("norm_single_agents_test.rds")
norm_data <- normalizeData(test_data,
neg_control = "NC-1",
pos_control = "PC1-D1-S",
trim = "T")
normalization_test <- (norm_data$INTENSITY - norm_data$PC) / (norm_data$NC - norm_data$PC)
normalization_test[normalization_test > 1 ] <- 1
normalization_test[normalization_test < 0 ] <- 0
expect_identical(normalization_test, norm_data$normalized_intensity)
})
test_that("normalizeData outputs library and anchor data for C treatments", {
test_data <- readRDS("combo_norm_data_test.rds")
norm_data <- normalizeData(test_data,
neg_control = "NC-1",
pos_control = "B")
c_treatments <- norm_data[norm_data$treatment == 'C',]
expect_false(any(is.na(c_treatments$DRUG_ID_lib)))
expect_false(any(is.na(c_treatments$CONC)))
expect_false(any(is.na(c_treatments$lib_drug)))
expect_false(any(is.na(c_treatments$dose)))
expect_false(any(is.na(c_treatments$treatment)))
expect_false(any(is.na(c_treatments$DRUG_ID_anch)))
expect_false(any(is.na(c_treatments$CONC_anch)))
expect_false(any(is.na(c_treatments$anchor)))
})
test_that("normalizeComboData points to and gives same results as normalizeData", {
test_data <- readRDS("combo_norm_data_test.rds")
norm_data <- normalizeData(test_data,
neg_control = "NC-1",
pos_control = "B")
norm_combo_data <- normalizeComboData(test_data,
neg_control = "NC-1",
pos_control = "B")
norm_data$time_stamp <- NULL
norm_combo_data$time_stamp <- NULL
expect_identical(norm_data, norm_combo_data)
})
CancerRxGene/gdscIC50 documentation built on Oct. 6, 2022, 2:40 a.m.
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context("Test calcTagMean")
test_that("calcTagMean", {
test_data <- rbind(
data.frame(SCAN_ID = 101, TAG = "NC1", INTENSITY = c(4648, 9846, 1563, 1519)),
data.frame(SCAN_ID = 101, TAG = "NC2", INTENSITY = c(4648, 9846, 1563, 1519)),
data.frame(SCAN_ID = 102, TAG = "NC2", INTENSITY = c(1672, 4366, 1651, 6527)),
data.frame(SCAN_ID = 103, TAG = "NC1", INTENSITY = c(6175, 1381, 4367, 6345)),
data.frame(SCAN_ID = 103, TAG = "NC2", INTENSITY = c(NA, NA, NA, NA))
)
# No tag at all of "foo"
expect_error(calcTagMean(test_data, "foo"),
"is not present for some or all of the SCAN_IDs in your data")
# No NC1 for scan 102
expect_error(calcTagMean(test_data, "NC1"),
"is not present for some or all of the SCAN_IDs in your data")
# Mean of NC2 for scan 103 is NaN
expect_error(calcTagMean(test_data, "NC2"),
"has a mean of NaN for some or all of the SCAN_IDs in your data")
})
context("Test normalize data")
test_that("normalizeData returns a data frame for single agent only data", {
# data("gdsc_example")
test_data <- readRDS("norm_single_agents_test.rds")
norm_data <- normalizeData(test_data,
neg_control = "NC-1",
pos_control = "PC1-D1-S")
expect_true(is.data.frame(norm_data))
expected_names <- c("SCAN_ID",
"BARCODE",
"RESEARCH_PROJECT",
"DATE_CREATED",
"DRUGSET_ID",
"CELL_LINE_NAME",
"CELL_ID",
"MASTER_CELL_ID",
"COSMIC_ID",
"POSITION",
"DRUG_ID_lib",
"CONC",
"INTENSITY",
"lib_drug",
"dose",
"treatment",
"NC",
"PC",
"normalized_intensity",
"norm_neg_pos",
"time_stamp",
"sw_version")
expect_named(norm_data, expected_names)
})
test_that("normalizeData returns a data frame with combination treatment
data with the right names", {
test_data <- readRDS("combo_norm_data_test.rds")
norm_data <- normalizeData(test_data,
neg_control = "NC-1",
pos_control = "B")
expect_true(is.data.frame(norm_data))
expected_names <- c("SCAN_ID",
"BARCODE",
"RESEARCH_PROJECT",
"DATE_CREATED",
"DRUGSET_ID",
"CELL_LINE_NAME",
"CELL_ID",
"MASTER_CELL_ID",
"COSMIC_ID",
"POSITION",
"DRUG_ID_lib",
"CONC",
"INTENSITY",
"lib_drug",
"dose",
"treatment",
"DRUG_ID_anch",
"CONC_anch",
"anchor",
"NC",
"PC",
"normalized_intensity",
"norm_neg_pos",
"time_stamp",
"sw_version")
expect_named(norm_data, expected_names)
})
test_that("normalizeData maintains data mappings to barcode", {
test_data <- readRDS("norm_single_agents_test.rds")
norm_data <- normalizeData(test_data)
expect_identical(unique(test_data[test_data$BARCODE == 1234, "RESEARCH_PROJECT"]),
unique(norm_data[norm_data$BARCODE == 1234, "RESEARCH_PROJECT"]))
expect_identical(unique(test_data[test_data$BARCODE == 1234, "SCAN_ID"]),
unique(norm_data[norm_data$BARCODE == 1234, "SCAN_ID"]))
expect_identical(unique(test_data[test_data$BARCODE == 1234, "COSMIC_ID"]),
unique(norm_data[norm_data$BARCODE == 1234, "COSMIC_ID"]))
expect_identical(unique(test_data[test_data$BARCODE == 1234, "CELL_LINE_NAME"]),
unique(norm_data[norm_data$BARCODE == 1234, "CELL_LINE_NAME"]))
expect_identical(unique(test_data[test_data$BARCODE == 1234, "CELL_ID"]),
unique(norm_data[norm_data$BARCODE == 1234, "CELL_ID"]))
expect_identical(unique(test_data[test_data$BARCODE == 1234, "MASTER_CELL_ID"]),
unique(norm_data[norm_data$BARCODE == 1234, "MASTER_CELL_ID"]))
expect_identical(unique(test_data[test_data$BARCODE == 1234, "DRUGSET_ID"]),
unique(norm_data[norm_data$BARCODE == 1234, "DRUGSET_ID"]))
expect_identical(unique(test_data[test_data$BARCODE == 5678, "RESEARCH_PROJECT"]),
unique(norm_data[norm_data$BARCODE == 5678, "RESEARCH_PROJECT"]))
expect_identical(unique(test_data[test_data$BARCODE == 5678, "SCAN_ID"]),
unique(norm_data[norm_data$BARCODE == 5678, "SCAN_ID"]))
expect_identical(unique(test_data[test_data$BARCODE == 5678, "COSMIC_ID"]),
unique(norm_data[norm_data$BARCODE == 5678, "COSMIC_ID"]))
expect_identical(unique(test_data[test_data$BARCODE == 5678, "CELL_LINE_NAME"]),
unique(norm_data[norm_data$BARCODE == 5678, "CELL_LINE_NAME"]))
expect_identical(unique(test_data[test_data$BARCODE == 5678, "CELL_ID"]),
unique(norm_data[norm_data$BARCODE == 5678, "CELL_ID"]))
expect_identical(unique(test_data[test_data$BARCODE == 5678, "MASTER_CELL_ID"]),
unique(norm_data[norm_data$BARCODE == 5678, "MASTER_CELL_ID"]))
expect_identical(unique(test_data[test_data$BARCODE == 5678, "DRUGSET_ID"]),
unique(norm_data[norm_data$BARCODE == 5678, "DRUGSET_ID"]))
intensity_test <- merge(
test_data[, c("SCAN_ID", "POSITION", "INTENSITY")],
norm_data[, c("SCAN_ID", "POSITION", "INTENSITY")],
by = c("SCAN_ID", "POSITION"))
expect_identical(intensity_test$INTENSITY.x, intensity_test$INTENSITY.y)
})
test_that("normalizeData calculates correct mean values for negative controls", {
test_data <- readRDS("norm_single_agents_test.rds")
norm_data <- normalizeData(test_data,
neg_control = "NC-1",
pos_control = "PC1-D1-S")
expect_length(unique(norm_data[norm_data$SCAN_ID == 1199, "NC"]), 1)
expect_equal(unique(norm_data[norm_data$SCAN_ID == 1199, "NC"]),
mean(test_data[test_data$SCAN_ID == 1199 & test_data$TAG == 'NC-1',
"INTENSITY"]
)
)
expect_length(unique(norm_data[norm_data$SCAN_ID == 1299, "NC"]), 1)
expect_equal(unique(norm_data[norm_data$SCAN_ID == 1299, "NC"]),
mean(test_data[test_data$SCAN_ID == 1299 & test_data$TAG == 'NC-1',
"INTENSITY"]
)
)
})
test_that("normalizeData calculates correct mean values for positive controls", {
test_data <- readRDS("norm_single_agents_test.rds")
# Test PCs with different values
norm_data <- normalizeData(test_data,
neg_control = "NC-1",
pos_control = "B")
expect_length(unique(norm_data[norm_data$SCAN_ID == 1199, "PC"]), 1)
expect_equal(unique(norm_data[norm_data$SCAN_ID == 1199, "PC"]),
mean(test_data[test_data$SCAN_ID == 1199 & test_data$TAG == 'B',
"INTENSITY"]
)
)
expect_length(unique(norm_data[norm_data$SCAN_ID == 1299, "PC"]), 1)
expect_equal(unique(norm_data[norm_data$SCAN_ID == 1299, "PC"]),
mean(test_data[test_data$SCAN_ID == 1299 & test_data$TAG == 'B',
"INTENSITY"]
)
)
})
test_that("normalizeData calculates the normalized intensity correctly",{
test_data <- readRDS("norm_single_agents_test.rds")
norm_data <- normalizeData(test_data,
neg_control = "NC-1",
pos_control = "PC1-D1-S",
trim = "F")
normalization_test <- (norm_data$INTENSITY - norm_data$PC) / (norm_data$NC - norm_data$PC)
expect_identical(normalization_test, norm_data$normalized_intensity)
})
test_that("normalizeData trims the normalized intensity correctly",{
test_data <- readRDS("norm_single_agents_test.rds")
norm_data <- normalizeData(test_data,
neg_control = "NC-1",
pos_control = "PC1-D1-S",
trim = "T")
normalization_test <- (norm_data$INTENSITY - norm_data$PC) / (norm_data$NC - norm_data$PC)
normalization_test[normalization_test > 1 ] <- 1
normalization_test[normalization_test < 0 ] <- 0
expect_identical(normalization_test, norm_data$normalized_intensity)
})
test_that("normalizeData outputs library and anchor data for C treatments", {
test_data <- readRDS("combo_norm_data_test.rds")
norm_data <- normalizeData(test_data,
neg_control = "NC-1",
pos_control = "B")
c_treatments <- norm_data[norm_data$treatment == 'C',]
expect_false(any(is.na(c_treatments$DRUG_ID_lib)))
expect_false(any(is.na(c_treatments$CONC)))
expect_false(any(is.na(c_treatments$lib_drug)))
expect_false(any(is.na(c_treatments$dose)))
expect_false(any(is.na(c_treatments$treatment)))
expect_false(any(is.na(c_treatments$DRUG_ID_anch)))
expect_false(any(is.na(c_treatments$CONC_anch)))
expect_false(any(is.na(c_treatments$anchor)))
})
test_that("normalizeComboData points to and gives same results as normalizeData", {
test_data <- readRDS("combo_norm_data_test.rds")
norm_data <- normalizeData(test_data,
neg_control = "NC-1",
pos_control = "B")
norm_combo_data <- normalizeComboData(test_data,
neg_control = "NC-1",
pos_control = "B")
norm_data$time_stamp <- NULL
norm_combo_data$time_stamp <- NULL
expect_identical(norm_data, norm_combo_data)
})
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