context("raw data parsing")
anaInfo <- getTestAnaInfo()
anaInfoOne <- getTestAnaInfo()[4, ]
fList <- getTestFeatures(noiseThrInt = 1E5)
fgOpenMS <- groupFeatures(fList, "openms")
test_that("TICs", {
checkmate::expect_data_table(getTICs(anaInfoOne))
expect_equal(unique(getTICs(anaInfoOne, MSLevel = 2)[["MSLevel"]]), 2)
expect_equal(colnames(getTICs(anaInfoOne)), c("analysis", "group", "ret", "MSLevel", "intensity"))
expect_equal(nrow(getTICs(anaInfoOne)), 759)
expect_lt(nrow(getTICs(anaInfoOne, retentionRange = c(10, 200))), 759)
checkmate::expect_data_table(getTICs(fList, MSLevel = 2))
checkmate::expect_data_table(getTICs(fgOpenMS))
})
test_that("BPCs", {
checkmate::expect_data_table(getBPCs(anaInfoOne))
expect_equal(colnames(getBPCs(anaInfoOne)), c("analysis", "group", "ret", "MSLevel", "mz", "intensity"))
expect_equal(nrow(getBPCs(anaInfoOne)), 759)
checkmate::expect_data_table(getBPCs(fList))
checkmate::expect_data_table(getBPCs(fgOpenMS))
})
test_that("test plot TICs and BPCs", {
expect_doppel("raw-tic", function() plotTICs(anaInfoOne))
expect_doppel("raw-tic-col", function() plotTICs(fList, colourBy = "rGroups", MSLevel = 1))
expect_doppel("raw-ms2", function() plotTICs(fgOpenMS[2:4, ], colourBy = "rGroups", MSLevel = 2))
expect_doppel("raw-bpc", function() plotBPCs(anaInfo[2:3, ]))
expect_doppel("raw-tic-feat", function() plotTICs(fList[1, ]))
expect_doppel("raw-tic-fg", function() plotTICs(fgOpenMS[1, ]))
})
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