Nothing
# dup_snps_in_overlapping_genes -----------------------------------------------#
# dup_snps_in_overlapping_genes -----------------------------------------------#
test_that("dup_snps_in_overlapping_genes() works as expected when given valid inputs", {
temp_gff <- read_gff(prewas::gff)
temp_gff <- temp_gff[1:4, , drop = FALSE]
temp_bin_mat <- matrix(c(0, 0, 1), nrow = 7, ncol = 3)
colnames(temp_bin_mat) <- c("t1", "t2", "t3")
row.names(temp_bin_mat) <- c(25:31)
temp_dup_mat <- dup_snps_in_overlapping_genes(temp_bin_mat, temp_gff)
expect_equal(nrow(temp_dup_mat), 22)
expect_equal(ncol(temp_dup_mat), 3)
})
test_that("dup_snps_in_overlapping_genes() gives error when given invalid inputs", {
expect_error(dup_snps_in_overlapping_genes("foo", matrix(0, 10, 10)))
expect_error(dup_snps_in_overlapping_genes(matrix(0, 10, 10), "foo"))
expect_error(dup_snps_in_overlapping_genes(matrix(0, 10, 10),
matrix(0, 10, 10)))
})
# dup_snps_in_overlapping_genes_snpeff ----------------------------------------#
test_that("dup_snps_in_overlapping_genes_snpeff() works as expected when given valid inputs", {
temp_bin_mat <- matrix(c(0, 0, 1), nrow = 7, ncol = 3)
colnames(temp_bin_mat) <- c("t1", "t2", "t3")
row.names(temp_bin_mat) <- c(25:31)
temp_predicted_impact <-
c("LOW", "LOW|HIGH", "MODERATE", "HIGH|HIGH", "MODIFIER", "LOW", "LOW|HIGH")
temp_gene <- c("gene1",
"gene2|gene3",
"gene4",
"gene5|gene6",
"gene7",
"gene8",
"gene9|gene10")
temp_dup_mat <-
dup_snps_in_overlapping_genes_snpeff(temp_bin_mat,
temp_predicted_impact,
temp_gene)
expect_equal(nrow(temp_dup_mat$bin_mat_dup), 10)
expect_equal(length(temp_dup_mat$predicted_impact_split), 10)
expect_equal(ncol(temp_dup_mat$bin_mat_dup), 3)
})
test_that("dup_snps_in_overlapping_genes() gives error when given invalid inputs", {
temp_bin_mat <- matrix(c(0, 0, 1), nrow = 7, ncol = 3)
colnames(temp_bin_mat) <- c("t1", "t2", "t3")
row.names(temp_bin_mat) <- c(25:31)
temp_predicted_impact <-
c("LOW", "LOW|HIGH", "MODERATE", "HIGH|HIGH", "MODIFIER", "LOW", "LOW|HIGH")
temp_gene <- c("gene1",
"gene2|gene3",
"gene4",
"gene5|gene6",
"gene7",
"gene8",
"gene9|gene10")
temp_dup_mat <- dup_snps_in_overlapping_genes_snpeff(temp_bin_mat,
temp_predicted_impact,
temp_gene)
expect_error(dup_snps_in_overlapping_genes_snpeff("foo", "foo", "foo"))
expect_error(dup_snps_in_overlapping_genes_snpeff(matrix(0, 10, 10),
"foo",
"foo"))
})
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