85 lines
2.6 KiB
R
85 lines
2.6 KiB
R
context("Auxiliary functions to greedyMix")
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# Defining the relative path to current inst -----------------------------------
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path_inst <- system.file("extdata", "", package = "rBAPS")
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# Reading datasets -------------------------------------------------------------
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baps_diploid <- read.delim(
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file = file.path(path_inst, "BAPS_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("Processing files through greedyMix")
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raw_fasta <- importFile(
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data = file.path(path_inst, "FASTA_clustering_haploid.fasta"),
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format = "FASTA"
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)
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raw_vcf <- importFile(
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data = file.path(path_inst, "vcf_example.vcf"),
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format = "VCF",
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verbose = FALSE
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)
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raw_bam <- importFile(
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data = file.path(path_inst, "bam_example.bam"),
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format = "BAM",
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)
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test_that("Files are imported correctly", {
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expect_equal(dim(raw_fasta), c(5, 99))
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expect_equal(dim(raw_vcf), c(variants = 2, fix_cols = 8, gt_cols = 3))
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expect_error(
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importFile(
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data = paste(path_inst, "sam_example.sam", sep = "/"),
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format = "SAM",
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)
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)
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expect_equal(length(raw_bam[[1]]), 13)
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})
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test_that("greedyMix() fails successfully", {
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expect_error(greedyMix(file.path(path_inst, "vcf_example.vcf")))
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expect_error(greedyMix(file.path(path_inst, "bam_example.bam")))
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})
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test_that("greedyMix() works when it should", {
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baps_file <- file.path(path_inst, "BAPS_clustering_diploid.txt")
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genepop_file <- file.path(path_inst, "GenePop.txt")
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fasta_file <- file.path(path_inst, "FASTA_clustering_haploid.fasta")
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greedy_baps <- greedyMix(baps_file, "BAPS")
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greedy_genepop <- greedyMix(genepop_file, "GenePop") # FIXME: doesn't match MATLAB output
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expect_type(greedy_baps, "list")
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expect_length(greedy_baps, 10L)
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})
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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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})
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