Nothing
context("testCoercionMethods")
check_biobase <- function() {
if (!requireNamespace("Biobase", quietly = TRUE)) {
skip("Biobase not available")
}
}
test_that("can coerce matrixData to ExpressionSet", {
check_biobase()
require(Biobase)
mD <- matrixData(
main=data.frame(a=1:3, b=6:8),
annotCols=data.frame(b=c('a','b','c')),
annotRows=data.frame(x=factor(c('1','1'))))
expect_s4_class(as(mD, "ExpressionSet"), "ExpressionSet")
})
test_that("can ExpressionSet to matrixData", {
check_biobase()
require(Biobase)
eSet <- Biobase::ExpressionSet(matrix(1:10, ncol = 2))
expect_s4_class(as(eSet, "matrixData"), "matrixData")
})
# TODO: check if the fact that the rownames are different is relevant
test_that("matrixData coherced back and forth to Expression set is identical", {
check_biobase()
require(Biobase)
mD <- matrixData(
main=data.frame(a=1:3, b=6:8),
annotCols=data.frame(b=c('a','b','c')),
annotRows=data.frame(x=factor(c('1','1'))))
eSet2 <- as(mD, "ExpressionSet")
mD2 <- as(eSet2, "matrixData")
expect_s4_class(mD2, "matrixData")
expect_true(all(main(mD) == main(mD2)))
})
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