54 lines
No EOL
1.5 KiB
R
54 lines
No EOL
1.5 KiB
R
context("Auxiliary functions to greedyMix")
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# Defining the relative path to current inst ------------- #
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if (interactive()) {
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path_inst <- "../../inst/ext/"
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} else {
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path_inst <- "inst/ext/"
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}
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baps_diploid <- read.delim(
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file = file.path(path_inst, "BAPS_format_clustering_diploid.txt"),
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sep = " ",
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header = FALSE
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)
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test_that("handleData works as expected", {
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data_obs <- handleData(baps_diploid)$newData
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data_exp <- matrix(
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c(
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-9, 1, 2, 1, 1, 1, 2, 1, 2, 2, 1,
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-9, 1, 1, 2, 2, 2, 1, 1, 1, 2, 1,
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3, 2, 2, 3, 2, -9, 3, 1, 2, 1, 2,
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2, 1, 2, 1, 2, -9, 1, 1, 1, 1, 2,
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3, 1, 1, 1, 2, 1, 1, 2, -9, 1, 3,
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3, 1, 2, 1, 1, 1, 2, 1, -9, 2, 3,
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1, 1, 1, 2, 2, 2, 1, 1, 1, 2, 4,
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3, 2, 2, 3, 2, 2, 3, 1, 2, 1, 4,
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2, 1, 2, 1, -9, 1, 1, 1, 1, 1, 5,
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3, 1, 1, 1, -9, 1, 1, 2, 1, 1, 5
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),
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nrow = 10, byrow = TRUE
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)
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colnames(data_exp) <- colnames(data_obs)
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expect_equal(data_obs, data_exp)
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})
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context("Opening files on greedyMix/load_fasta")
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# # TODO: needs #12 to be fixed before this can be done without user intervention
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# greedyMix(
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# tietue = "inst/ext/ExamplesDataFormatting/Example data in BAPS format for clustering of diploid individuals.txt",
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# format = "BAPS",
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# savePreProcessed = FALSE
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# ) # Upper bounds 100 100
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# TODO #16: replace with load_fasta()
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context("Linkage")
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test_that("Linkages are properly calculated", {
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Y <- c(0.5, 0.3, 0.6, 0.3, 0.3, 0.2, 0.3, 0.3, 0.3, 0.5)
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expect_equal(
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object = linkage(Y),
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expected = matrix(c(2, 1, 7, 8, 4, 3, 5, 6, .2, .3, .3, .6), ncol=3)
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)
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}) |