Nothing
context("reset.R functions")
skip_if(setup_failed)
test_that('reset.R: gene level data', {
test_t_obj <- t_obj
test_t_reset <- resetDGEobj(test_t_obj)
# object validation
expect_s3_class(test_t_reset, "DGEobj")
expect_equivalent(showMeta(test_t_reset), showMeta(test_t_obj))
# validate level is gene before and after reset
test_t_meta <- showMeta(test_t_obj)
expect_equal("gene", test_t_meta$Value[3])
expect_equal(attr(test_t_obj, "level"), "gene")
test_t_meta_reset <- showMeta(test_t_reset)
expect_equal("gene", test_t_meta_reset$Value[3])
expect_equal(attr(test_t_reset, "level"), "gene")
# reset after subsetting
expect_equal(dim(test_t_obj), t_dim)
test_t_obj <- test_t_obj[c(1:10), ]
test_t_reset <- resetDGEobj(test_t_obj)
expect_equal(dim(test_t_reset), c(1000, 48))
# check names after reset
expect_named(test_t_obj, c('counts_orig', 'counts', 'design_orig', 'design', 'geneData_orig',
'geneData', 'granges_orig', 'granges', 'DGEList', 'ReplicateGroupDesign',
'ReplicateGroupDesign_Elist', 'ReplicateGroupDesign_fit',
'ReplicateGroupDesign_fit_cm', 'ReplicateGroupDesign_fit_cf',
'BDL_vs_Sham', 'EXT1024_vs_BDL', 'Nint_vs_BDL', 'Sora_vs_BDL'))
expect_named(test_t_reset, c("counts_orig", "counts", "design_orig", "design",
"geneData_orig", "geneData", "granges_orig", "granges"))
# testing t_obj with rm item
test_t_obj <- rmItem(test_t_obj, "BDL_vs_Sham")
expect_false("BDL_vs_Sham" %in% names(test_t_obj))
test_t_reset <- resetDGEobj(test_t_obj)
expect_false("BDL_vs_Sham" %in% names(test_t_reset)) # should not be restored
# testing t_obj with add item
test_t_obj <- addItem(test_t_obj,
item = 'Fred Flintstone',
itemName = 'Cartoon',
itemType = 'meta',
itemAttr = list('MyAttribute' = 'testObject'))
test_t_attr <- getAttributes(test_t_obj)
expect_equivalent(attributes(test_t_obj$Cartoon), 'testObject')
expect_true("Cartoon" %in% names(test_t_obj))
test_t_reset <- resetDGEobj(test_t_obj)
expect_null(attributes(test_t_reset$Cartoon), 'testObject')
expect_false("Cartoon" %in% names(test_t_reset)) # check if removed
# testing t_obj after class change
test_t_obj <- as.list.DGEobj(test_t_obj)
expect_equal(class(test_t_obj), "list")
# coerce back into DGEobj, expect reset to work
class(test_t_obj) <- "DGEobj"
expect_silent(resetDGEobj(test_t_obj))
})
# test isoform level data
test_that('reset.R: isoform level data', {
test_t_obj <- t_isoform_obj
test_t_reset <- resetDGEobj(test_t_obj)
# object validation
expect_s3_class(test_t_reset, "DGEobj")
expect_equivalent(showMeta(test_t_reset), showMeta(test_t_obj))
# validate level is isoform before and after reset
test_t_meta <- showMeta(test_t_obj)
expect_equal("isoform", test_t_meta$Value[3])
expect_equal(attr(test_t_obj, "level"), "isoform")
test_t_meta_reset <- showMeta(test_t_reset)
expect_equal("isoform", test_t_meta_reset$Value[3])
expect_equal(attr(test_t_reset, "level"), "isoform")
# reset after subsetting
test_t_dim <- dim(t_isoform_obj)
expect_equal(dim(test_t_obj),test_t_dim)
test_t_obj <- test_t_obj[c(1:10), ]
test_t_reset <- resetDGEobj(test_t_obj)
expect_equal(dim(test_t_reset), test_t_dim)
# check names after reset
expect_named(test_t_obj, c("intensities_orig", "intensities", "design_orig",
"design", "isoformData_orig", "isoformData"))
expect_named(test_t_reset, c("intensities_orig", "intensities", "design_orig",
"design", "isoformData_orig", "isoformData"))
# testing test_t_obj with rm item
test_t_obj <- rmItem(test_t_obj, "isoformData")
expect_false("isoformData" %in% names(test_t_obj))
test_t_reset <- resetDGEobj(test_t_obj)
expect_true("isoformData" %in% names(test_t_reset)) # check if restored
# testing test_t_obj with add item
test_t_obj <- addItem(test_t_obj,
item = 'Fred Flintstone',
itemName = 'Cartoon',
itemType = 'meta',
itemAttr = list('MyAttribute' = 'testObject'))
test_t_attr <- getAttributes(test_t_obj)
expect_equivalent(attributes(test_t_obj$Cartoon), 'testObject')
expect_true("Cartoon" %in% names(test_t_obj))
test_t_reset <- resetDGEobj(test_t_obj)
expect_null(attributes(test_t_reset$Cartoon), 'testObject')
expect_false("Cartoon" %in% names(test_t_reset)) # check if removed
# testing test_t_obj after class change
test_t_obj <- as.list.DGEobj(test_t_obj)
expect_equal(class(test_t_obj), "list")
# coerce back into DGEobj, expect reset to work
class(test_t_obj) <- "DGEobj"
expect_silent(resetDGEobj(test_t_obj))
})
# test exon level data
test_that('reset.R: exon level data', {
test_t_obj <- t_exon_obj
test_t_reset <- resetDGEobj(test_t_obj)
# object validation
expect_s3_class(test_t_reset, "DGEobj")
expect_equivalent(showMeta(test_t_reset), showMeta(test_t_obj))
# validate level is exon before and after reset
test_t_meta <- showMeta(test_t_obj)
expect_equal("exon", test_t_meta$Value[3])
expect_equal(attr(test_t_obj, "level"), "exon")
test_t_meta_reset <- showMeta(test_t_reset)
expect_equal("exon", test_t_meta_reset$Value[3])
expect_equal(attr(test_t_reset, "level"), "exon")
# reset after subsetting
test_t_dim <- dim(t_exon_obj)
expect_equal(dim(test_t_obj), test_t_dim)
test_t_obj <- test_t_obj[c(1:10), ]
test_t_reset <- resetDGEobj(test_t_obj)
expect_equal(dim(test_t_reset), test_t_dim)
# check names after reset
expect_named(test_t_obj, c('counts_orig', 'counts', 'design_orig', 'design', 'exonData_orig',
'exonData', 'granges_orig', 'granges'))
expect_named(test_t_reset, c("counts_orig", "counts", "design_orig", "design",
"exonData_orig", "exonData", "granges_orig", "granges"))
# testing test_t_obj with rm item
test_t_obj <- rmItem(test_t_obj, "granges")
expect_false("granges" %in% names(test_t_obj))
test_t_reset <- resetDGEobj(test_t_obj)
expect_true("granges" %in% names(test_t_reset)) # check if persists
# testing test_t_obj with add item
test_t_obj <- addItem(test_t_obj,
item = 'Fred Flintstone',
itemName = 'Cartoon',
itemType = 'meta',
itemAttr = list('MyAttribute' = 'testObject'))
test_t_attr <- getAttributes(test_t_obj)
expect_equivalent(attributes(test_t_obj$Cartoon), 'testObject')
expect_true("Cartoon" %in% names(test_t_obj))
test_t_reset <- resetDGEobj(test_t_obj)
expect_null(attributes(test_t_reset$Cartoon), 'testObject')
expect_false("Cartoon" %in% names(test_t_reset)) # check if removed
# testing test_t_obj after class change
test_t_obj <- as.list.DGEobj(test_t_obj)
expect_equal(class(test_t_obj), "list")
# coerce back into DGEobj, expect reset to work
class(test_t_obj) <- "DGEobj"
expect_silent(resetDGEobj(test_t_obj))
})
# test protein level data
test_that('reset.R: protein level data', {
test_t_obj <- t_protein_obj
test_t_reset <- resetDGEobj(test_t_obj)
# object validation
expect_s3_class(test_t_reset, "DGEobj")
expect_equivalent(showMeta(test_t_reset), showMeta(test_t_obj))
# validate level is protein before and after reset
test_t_meta <- showMeta(test_t_obj)
expect_equal("protein", test_t_meta$Value[3])
expect_equal(attr(test_t_obj, "level"), "protein")
test_t_meta_reset <- showMeta(test_t_reset)
expect_equal("protein", test_t_meta_reset$Value[3])
expect_equal(attr(test_t_reset, "level"), "protein")
# reset after subsetting
test_t_dim <- dim(t_protein_obj)
expect_equal(dim(test_t_obj), test_t_dim)
test_t_obj <- test_t_obj[c(1:10), ]
test_t_reset <- resetDGEobj(test_t_obj)
expect_equal(dim(test_t_reset), test_t_dim)
# check names after reset
expect_named(test_t_obj, c('intensities_orig', 'intensities', 'design_orig',
'design', 'proteinData_orig', 'proteinData'))
expect_named(test_t_reset, c('intensities_orig', 'intensities', 'design_orig',
'design', 'proteinData_orig', 'proteinData'))
# testing test_t_obj with rm item
test_t_obj <- rmItem(test_t_obj, "intensities")
expect_false("intensities" %in% names(test_t_obj))
test_t_reset <- resetDGEobj(test_t_obj)
expect_true("intensities" %in% names(test_t_reset)) # check if persists
# testing test_t_obj with add item
test_t_obj <- addItem(test_t_obj,
item = 'Fred Flintstone',
itemName = 'Cartoon',
itemType = 'meta',
itemAttr = list('MyAttribute' = 'testObject'))
test_t_attr <- getAttributes(test_t_obj)
expect_equivalent(attributes(test_t_obj$Cartoon), 'testObject')
expect_true("Cartoon" %in% names(test_t_obj))
test_t_reset <- resetDGEobj(test_t_obj)
expect_null(attributes(test_t_reset$Cartoon), 'testObject')
expect_false("Cartoon" %in% names(test_t_reset)) # check if removed
# testing test_t_obj after class change
test_t_obj <- as.list.DGEobj(test_t_obj)
expect_equal(class(test_t_obj), "list")
# coerce back into DGEobj, expect reset to work
class(test_t_obj) <- "DGEobj"
expect_silent(resetDGEobj(test_t_obj))
})
# misc tests
test_that('reset.R: misc', {
test_t_obj <- t_obj
test_t_reset <- resetDGEobj(t_obj)
#test invalid level
expect_error(test_t_obj <- initDGEobj(primaryAssayData = t_obj$counts,
rowData = t_obj$geneData,
colData = t_obj$design,
level = "Fred Flinstone"),
regexp = "The specified level must be one of: gene, exon, isoform, protein, affy")
# testing t_obj with new attributes
new_attributes <- list("attribute1" = runif(100, min = 0, max = 2), "attribute2" = LETTERS)
test_t_obj <- setAttributes(test_t_obj, new_attributes)
test_t_attr <- getAttributes(test_t_obj)
expect_true(exists('attribute1', where = getAttributes(test_t_obj)))
expect_setequal(test_t_attr$attribute2, LETTERS)
test_t_reset <- resetDGEobj(test_t_obj)
test_t_reset_attr <- getAttributes(test_t_reset)
expect_true(exists('attribute1', where = getAttributes(test_t_reset)))
expect_setequal(test_t_reset_attr$attribute2, LETTERS)
# testing t_obj without platformType (no longer required for reset)
test_t_obj <- setAttributes(t_obj, list("PlatformType" = NULL))
expect_s3_class(resetDGEobj(test_t_obj), "DGEobj")
# testing rm item with _orig
test_t_obj <- rmItem(test_t_obj, "counts_orig")
expect_false("counts_orig" %in% names(test_t_obj))
expect_error(resetDGEobj(test_t_obj),
regexp = 'The requested itemName should be in the DGEobj. Use names(dgeObj) to see the available items.',
fixed = TRUE)
})
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