Nothing
anno <- getAnalyteInfo(example_data)
test_that("`getAnalyteInfo()` generates correct objects", {
expect_s3_class(anno, "tbl_df")
expect_equal(dim(anno), c(getAnalytes(example_data, n = TRUE), 22L))
expect_setequal(anno$AptName, getAnalytes(example_data))
expect_equal(vapply(anno, typeof, ""),
c(AptName = "character",
SeqId = "character",
SeqIdVersion = "double",
SomaId = "character",
TargetFullName = "character",
Target = "character",
UniProt = "character",
EntrezGeneID = "character",
EntrezGeneSymbol = "character",
Organism = "character",
Units = "character",
Type = "character",
Dilution = "character",
PlateScale_Reference = "double",
CalReference = "double",
Cal_Example_Adat_Set001 = "double",
ColCheck = "character",
CalQcRatio_Example_Adat_Set001_170255 = "double",
QcReference_170255 = "double",
Cal_Example_Adat_Set002 = "double",
CalQcRatio_Example_Adat_Set002_170255 = "double",
Dilution2 = "double"))
})
test_that("`getAnalyteInfo()` error conditions are triggered", {
x <- example_data
attr(x, "Col.Meta") <- as.data.frame(attr(x, "Col.Meta"))
expect_error(
getAnalyteInfo(x),
"`Col.Meta` must be a `tbl_df`."
)
attr(x, "Col.Meta") <- NULL
expect_error(
getAnalyteInfo(x),
"`Col.Meta` is absent from ADAT."
)
})
test_that("`getAnalyteInfo()` warning if Col.Meta out-of-sync with features", {
# option 1; features in data but not in Col.Meta
x <- example_data
attr(x, "Col.Meta") <- head(attr(x, "Col.Meta"), -1L) # rm final row
expect_warning(
y <- getAnalyteInfo(x),
"Features inconsistent between `AptName` vs `SeqId` in `getAnalyteInfo()`.",
fixed = TRUE
)
# tibble with NAs for missing features
n <- getAnalytes(x, n = TRUE)
expect_equal(dim(y), c(n, 22L))
# all NAs except for 2 columns (AptName, SeqId)
expect_equal(sum(!is.na(tail(y, 1L))), 2)
# option 2; features in Col.Meta but not in data
# rename final column
x <- example_data
attr(x, "Col.Meta")[n + 1L, ] <- attr(x, "Col.Meta")[n, ] # add dummy feature
attr(x, "Col.Meta")[n + 1L, 1L] <- "9999-99"
expect_warning(
y <- getAnalyteInfo(x),
"Features inconsistent between `AptName` vs `SeqId` in `getAnalyteInfo()`.",
fixed = TRUE
)
# no NAs; extra 9999-99 feature dropped
expect_equal(dim(y), c(n, 22L))
})
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