Nothing
data("scp1")
test_that("rowDataToDF", {
## Correct use
## single assay
test <- rowDataToDF(scp1, i = "190321S_LCA10_X_FP97AG", vars = "peptide")
expect_identical(nrow(test), nrow(scp1[[1]]))
expect_identical(dimnames(test), list(rownames(scp1[[1]]), c("peptide", ".assay", ".rowname")))
## Multiple assays
test <- rowDataToDF(scp1, i = 1:3, vars = "peptide")
expect_identical(nrow(test),
as.integer(sum(dims(scp1)[1, 1:3])))
expect_identical(dimnames(test),
list(unlist(lapply(1:3, function(x) rownames(scp1[[x]]))),
c("peptide", ".assay", ".rowname")))
## Variable not found
expect_error(rowDataToDF(scp1, i = 1:3, vars = "foo"),
regexp = "rowData variable\\(s\\) not found")
})
test_that("transferColData", {
## Correct Use
test <- transferColDataToAssay(scp1, i = "peptides")
expect_identical(colData(test[["peptides"]]),
colData(test)[colnames(test[["peptides"]]), ])
## Expect message
expect_message(transferColDataToAssay(test, i = "peptides"),
regexp = "colData is already present in assay")
})
test_that("aggregateFeaturesOverAssays", {
## Correct use
test <- aggregateFeaturesOverAssays(scp1, i = 1:3, fcol = "peptide",
name = paste0("peptides", 1:3),
fun = colSums)
expect_identical(test[["peptides1"]],
aggregateFeatures(scp1, i = 1, fcol = "peptide", name = "peptides1",
fun = colSums)[["peptides1"]])
al <- assayLink(test, "peptides1")
expect_identical(al@name, "peptides1")
expect_identical(al@from, "190321S_LCA10_X_FP97AG")
expect_identical(al@fcol, "peptide")
expect_identical(al@hits@from, 1:nrow(scp1[[1]]))
expect_identical(al@hits@to, as.integer(as.factor(rowData(scp1[[1]])$peptide)))
## Error: i and names must have same size
expect_error(aggregateFeaturesOverAssays(scp1, i = 1:3, fcol = "peptide",
name = "foo"),
regexp = "'i' and 'name' must have same length")
## Error: i and fcoli must have same size
expect_error(aggregateFeaturesOverAssays(scp1, i = 1:3, name = 1:3,
fcol = rep("peptide", 2)),
regexp = "'i' and 'fcol' must have same length")
##
})
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