context("preparing a data set")
test_that("ensure that samples and directories are included", {
expect_error(sleuth_prep(study_formula, study_mapping))
expect_error(sleuth_prep(3, study_mapping))
expect_error(sleuth_prep(study_mapping, 3))
})
test_that("normalization factors", {
expect_error(sleuth_prep(study_mapping, ~condition, norm_fun_counts = 3))
all_ones <- function(x) {
p <- ncol(x)
sf <- rep.int(1, p)
names(sf) <- colnames(x)
sf
}
result <- sleuth_prep(study_mapping, ~condition, norm_fun_counts = all_ones)
temp_result <- rep.int(1, nrow(study_mapping))
expect_equivalent(result$est_counts_sf, temp_result)
})
test_that("give a design matrix", {
design_matrix <- matrix(c(0, 0, 0, 1, 1, 1), ncol = 1)
expect_error(result <- sleuth_prep(study_mapping, design_matrix))
expect_error(sleuth_prep(study_mapping, design_matrix[1:5,]))
colnames(design_matrix) <- c('Intercept')
rownames(design_matrix) <- study_mapping$sample
result <- sleuth_prep(study_mapping, design_matrix)
expect_equal(result$design_matrix, design_matrix)
expect_equal(result$design_matrix, result$full_formula)
expect_equal(result$bs_summary, trans_test_data$bs_summary)
expect_equal(result$obs_norm, trans_test_data$obs_norm)
expect_equal(result$obs_norm_filt, trans_test_data$obs_norm_filt)
})
test_that("gene level", {
expect_error(result <- sleuth_prep(study_mapping, study_formula,
aggregation_column = "gene_name"))
result <- sleuth_prep(study_mapping, study_formula,
target_mapping = target_mapping,
aggregation_column = "gene_name")
expect_equal(result$bs_summary, gene_test_data$bs_summary)
expect_equal(result$obs_norm, gene_test_data$obs_norm)
expect_equal(result$obs_norm_filt, gene_test_data$obs_norm_filt)
expect_warning(result_incomplete <- sleuth_prep(study_mapping, study_formula,
target_mapping = incomplete_mapping,
aggregation_column = "gene_name"))
})
test_that(".N target mappings", {
expect_warning(result.N <- sleuth_prep(small_study_map,
target_mapping = small_target_mapping))
expect_warning(result.N <- sleuth_prep(small_study_map,
target_mapping = small_target_mapping,
aggregation_column = "gene_name"))
})
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