Nothing
context("DGEobj.utils - tests for runSVA.R functions")
skip_if(setup_failed)
test_that("runSVA.R: runSVA()", {
# method = leek
dgeObj_sva <- runSVA(dgeObj = t_obj1, designMatrixName = "ReplicateGroupDesign")
expect_s3_class(dgeObj_sva, "DGEobj")
# method = be
dgeObj_sva <- runSVA(dgeObj = t_obj1, designMatrixName = "ReplicateGroupDesign", method = "be")
expect_s3_class(dgeObj_sva, "DGEobj")
# method = be and custom na.sv
dgeObj_sva <- runSVA(dgeObj = t_obj1, designMatrixName = "ReplicateGroupDesign", n.sv = 10, method = "be")
expect_s3_class(dgeObj_sva, "DGEobj")
# method = be and large custom na.sv
expect_message(dgeObj_sva <- runSVA(dgeObj = t_obj1,
designMatrixName = "ReplicateGroupDesign",
n.sv = 10000, method = "be"),
regexp = "runSVA failed due to:")
expect_s3_class(dgeObj_sva, "DGEobj")
## dge
msg <- "dgeObj must be specified, be of class 'DGEobj', and should have a 'design' attribute."
expect_error(runSVA(),
regexp = msg)
expect_error(runSVA(NULL),
regexp = msg)
## designMatrixName
msg <- "designMatrixName must be specified, should be of class 'character', and must exist as an attribute on the dgeObj."
expect_error(runSVA(dgeObj = t_obj1, designMatrixName = NULL),
regexp = msg)
expect_error(runSVA(dgeObj = t_obj1),
regexp = msg)
expect_error(runSVA(dgeObj = t_obj1, designMatrixName = 123),
regexp = msg)
expect_error(runSVA(dgeObj = t_obj1, designMatrixName = c("ReplicateGroupDesign", "ReplicateGroupDesign")),
regexp = msg)
expect_error(runSVA(dgeObj = t_obj1, designMatrixName = "ReplicateGroupDesign", method = "xyz"),
regexp = "method must be one of 'leek' or 'be'.")
})
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