Nothing
context("test assessment functions")
test_that("pcr_efficiency calculates the correct intercept and slope", {
# make amount/dilution variable
amount <- rep(c(1, .5, .2, .1, .05, .02, .01), each = 3)
# calculate the standard curve
res <- pcr_efficiency(ct3,
amount = amount,
reference_gene = 'GAPDH')
log_amount <- log10(amount)
x <- with(ct3, c_myc - GAPDH)
c <- coef(lm(x ~ log_amount))
expect_equal(unname(c), unlist(res[, 2:3], use.names = FALSE))
gg <- pcr_efficiency(ct3,
amount = amount,
reference_gene = 'GAPDH',
plot = TRUE)
expect_identical(class(gg), c("gg", "ggplot"))
})
test_that("pcr_standard calculates the correct intercept and slope", {
# make amount/dilution variable
amount <- rep(c(1, .5, .2, .1, .05, .02, .01), each = 3)
# calculate the standard curve
res <- pcr_standard(ct3,
amount = amount)
log_amount <- log10(amount)
c <- coef(lm(ct3$c_myc ~ log_amount))
expect_equal(unlist(res[1, 2:3], use.names = FALSE), unname(c))
gg <- pcr_standard(ct3,
amount = amount,
plot = TRUE)
expect_identical(class(gg), c("gg", "ggplot"))
})
test_that("pcr_assess calls the correct methods", {
# default: standard_curve
# make amount/dilution variable
amount <- rep(c(1, .5, .2, .1, .05, .02, .01), each = 3)
# calculate the standard curve
res <- pcr_standard(ct3,
amount = amount)
log_amount <- log10(amount)
c <- coef(lm(ct3$c_myc ~ log_amount))
#expect_equal(unlist(res[1, 2:3], use.names = FALSE), unname(c))
# method: efficiency
# make amount/dilution variable
amount <- rep(c(1, .5, .2, .1, .05, .02, .01), each = 3)
# calculate the standard curve
res <- pcr_assess(ct3,
amount = amount,
reference_gene = 'GAPDH',
method = 'efficiency')
log_amount <- log10(amount)
x <- with(ct3, c_myc - GAPDH)
c <- coef(lm(x ~ log_amount))
expect_equal(unname(c), unlist(res[, 2:3], use.names = FALSE))
})
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