Nothing
test_that("everything grabs everything", {
expect_identical(mzML_everything, mzML_data)
})
test_that("everything got grabbed", {
expect_setequal(names(mzML_data), c("MS1", "MS2", "metadata", "TIC", "BPC"))
})
test_that("mzML MS1 data looks normal", {
# Check that there's data there at all
expect_gt(nrow(mzML_data$MS1), 0)
# Check that only expected columns exist
expect_setequal(names(mzML_data$MS1), c("rt", "mz", "int", "filename"))
# Check on column types
expect_type(mzML_data$MS1$rt, "double")
expect_type(mzML_data$MS1$mz, "double")
expect_type(mzML_data$MS1$int, "double")
expect_type(mzML_data$MS1$filename, "character")
# Check that the expected files were loaded
expect_length(unique(mzML_data$MS1$filename), 2)
expect_identical(unique(mzML_data$MS1$filename), basename(mzML_filenames[1:2]))
})
test_that("mzML MS2 data looks normal", {
# Check that there's data there at all
expect_gt(nrow(mzML_data$MS2), 0)
# Check that only expected columns exist
expect_setequal(names(mzML_data$MS2), c("rt", "fragmz", "premz", "voltage",
"int", "filename"))
# Check on column types
expect_type(mzML_data$MS2$rt, "double")
expect_type(mzML_data$MS2$fragmz, "double")
expect_type(mzML_data$MS2$premz, "double")
expect_type(mzML_data$MS2$int, "double")
expect_type(mzML_data$MS2$voltage, "integer")
expect_identical(unique(mzML_data$MS2$voltage), 35L)
expect_type(mzML_data$MS2$filename, "character")
# Check that the expected files were loaded
expect_length(unique(mzML_data$MS2$filename), 1)
expect_identical(unique(mzML_data$MS2$filename), basename(mzML_filenames[1]))
})
test_that("mzML BPC/TIC looks normal", {
# Check that there's data there at all
expect_gt(nrow(mzML_data$BPC), 0)
# Check that only expected columns exist
expect_setequal(names(mzML_data$BPC), c("rt", "int", "filename"))
# Check column types
expect_type(mzML_data$BPC$rt, "double")
expect_type(mzML_data$BPC$int, "double")
expect_type(mzML_data$BPC$filename, "character")
# Check that there's data there at all
expect_gt(nrow(mzML_data$TIC), 0)
# Check that only expected columns exist
expect_setequal(names(mzML_data$TIC), c("rt", "int", "filename"))
# Check column types
expect_type(mzML_data$TIC$rt, "double")
expect_type(mzML_data$TIC$int, "double")
expect_type(mzML_data$TIC$filename, "character")
# Check that TIC <= BPC
expect_true(all(mzML_data$BPC$int<=mzML_data$TIC$int))
})
test_that("multifile works", {
expect_length(unique(mzML_multi_data$MS1$filename), 3)
expect_length(unique(mzML_multi_data$TIC$filename), 3)
})
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