context("decontam")
test_that("decontam", {
data(esophagus, package="mia")
# setup of some mock data
colData(esophagus)$concentration <- c(1,2,3)
colData(esophagus)$control <- c(FALSE,FALSE,TRUE)
expect_warning(esophagus <- addContaminantQC(esophagus,
method = "frequency",
concentration = "concentration"))
expect_s4_class(rowData(esophagus)[,"isContaminant"],"DataFrame")
expect_warning(esophagus <- addNotContaminantQC(esophagus,
control = "control"))
expect_type(rowData(esophagus)[,"isNotContaminant"],"logical")
expect_warning(esophagus <- addNotContaminantQC(esophagus,
control = "control",
detailed = TRUE))
expect_s4_class(rowData(esophagus)[,"isNotContaminant"],"DataFrame")
})
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