tests/testthat/test_merge_p_values.r

In ActivePathways: Integrative Pathway Enrichment Analysis of Multivariate Omics Data

context("merge_p_values function")

test_list <- list(a=0.01, b=0.06, c=0.8, d=0.0001, e=0, f=1)
test_matrix <- matrix(c(0.01, 0.06, 0.08, 0.0001, 0, 1), ncol=2)

comparison_list <- test_list
comparison_list[[5]] = 1e-300

test_matrix = matrix(unlist(test_list), ncol = 2)
comparison_matrix = matrix(unlist(comparison_list), ncol = 2)

test_that("scores is a numeric matrix or list with valid p-values", {
   
   expect_error(merge_p_values(unlist(test_list), "Fisher"), NA)
   expect_error(merge_p_values(test_list, "Brown"), 
                "Brown's, DPM, Strube's, and Strube_directional methods cannot be used with a single list of p-values")
   expect_error(merge_p_values(unlist(test_list), "Brown"), 
                "Brown's, DPM, Strube's, and Strube_directional methods cannot be used with a single list of p-values")
   
   
   
   test_list[[1]] <- -0.1
   expect_error(merge_p_values(test_list), 'All values in scores must be in [0,1]', fixed=TRUE)
   test_list[[1]] <- 1.1
   expect_error(merge_p_values(test_list), 'All values in scores must be in [0,1]', fixed=TRUE)
   test_list[[1]] <- NA
   expect_error(merge_p_values(test_list), 'scores cannot contain missing values, we recommend replacing NA with 1 or removing')
   test_list[[1]] <- 'c'
   expect_error(merge_p_values(test_list), 'scores must be numeric')
   
   
   test_matrix[1, 1] <- NA
   expect_error(merge_p_values(test_matrix), 'scores cannot contain missing values, we recommend replacing NA with 1 or removing')
   test_matrix[1, 1] <- -0.1
   expect_error(merge_p_values(test_matrix), "All values in scores must be in [0,1]", fixed=TRUE)
   test_matrix[1, 1] <- 1.1
   expect_error(merge_p_values(test_matrix), "All values in scores must be in [0,1]", fixed=TRUE)
   test_matrix[1, 1] <- 'a'
   expect_error(merge_p_values(test_matrix), 'scores must be numeric')
   
   
})


test_direction_vector <- c(1,-1)


test_that("Merged p-values are correct", {
   
   this_tolerance = 1e-7
   answer1 = c(1.481551e-05, 4.167534e-299, 9.785148e-01)
   answer2 = c(2.52747e-05, 0.00000e+00, 9.73873e-01)
   answer3 = 7.147579e-296
   
   expect_equal(merge_p_values(test_matrix, "Fisher"), answer1, tolerance = this_tolerance)
   
   expect_equal(merge_p_values(test_matrix, "Brown"), answer2, tolerance = this_tolerance)
   
   expect_equal(merge_p_values(test_matrix[, 1, drop=FALSE], "Fisher"), test_matrix[, 1, drop=TRUE])
   expect_equal(merge_p_values(test_matrix[, 1, drop=FALSE], "Brown"), test_matrix[, 1, drop=TRUE])
   
   expect_equal(merge_p_values(test_list, "Fisher"), answer3, tolerance = this_tolerance)
   
   test_pval_vector <- c(0.05,0.01)
   test_direction_vector <- c(1,-1)
   constraints_vector1 <- c(-1,1)
   constraints_vector2 <- c(1,-1)
   
   expect_equal(merge_p_values(test_pval_vector,"Fisher_directional",test_direction_vector,constraints_vector1),
                merge_p_values(test_pval_vector,"Fisher_directional",test_direction_vector,constraints_vector2))
   
   inflated_pvals <- c(1, 1e-400)
   threshold_pvals <- c(1, 1e-300)
   expect_equal(merge_p_values(inflated_pvals), merge_p_values(threshold_pvals))
   
   inflated_pval_matrix = matrix(c(1, 1, 1e-320, 1e-310), ncol = 2)
   threshold_pval_matrix = matrix(c(1, 1, 1e-300, 1e-300), ncol = 2)
   expect_equal(merge_p_values(inflated_pval_matrix), merge_p_values(threshold_pval_matrix))
   
})


test_matrix <- matrix(c(0.01, 0.06, 0.08, 0.0001, 0, 1), ncol=2)
test_direction_matrix <- matrix(c(1,-1,1,-1,-1,1), ncol=2)
constraints_vector <- c(1,1)

colnames(test_matrix) <- c("RNA", "Protein") 
rownames(test_matrix) <- c("TP53", "CHRNA1","PTEN")

colnames(test_direction_matrix) <- colnames(test_matrix)
rownames(test_direction_matrix) <- rownames(test_matrix)

test_that("scores_direction and constraints_vector are valid", {
   
   expect_error(merge_p_values(test_matrix, "Fisher_directional",test_direction_matrix),'Both scores_direction and constraints_vector must be provided')
   expect_error(merge_p_values(test_matrix, "Fisher_directional",constraints_vector = constraints_vector),'Both scores_direction and constraints_vector must be provided')
   expect_error(merge_p_values(test_matrix, "Fisher_directional", test_direction_matrix, c(1,"b")), 'constraints_vector must be a numeric vector')
   expect_error(merge_p_values(test_matrix, "Fisher_directional", test_direction_matrix, c(1,0)), "scores_direction entries must be set to 0's for columns that do not contain directional information")
   expect_error(merge_p_values(test_matrix, "Fisher_directional", test_direction_matrix, c(1,5)), "constraints_vector must contain the values: 1, -1 or 0")
   
   test_dir <- as.vector(test_direction_matrix)
   expect_error(merge_p_values(test_matrix, "Fisher_directional", test_dir, c(1,1)), 'scores and scores_direction must be the same data type')
   
   test_dir <- test_direction_matrix
   test_dir[1,1] <- NA
   expect_error(merge_p_values(test_matrix, "Fisher_directional", test_dir, c(1,1)), 'scores_direction cannot contain missing values, we recommend replacing NA with 0 or removing')
   
   test_dir <- test_direction_matrix
   test_dir[1,1] <- 'a'
   expect_error(merge_p_values(test_matrix, "Fisher_directional", test_dir, c(1,1)), 'scores_direction must be numeric')
   
   test_dir <- test_direction_matrix
   colnames(test_dir) <- NULL
   expect_error(merge_p_values(test_matrix, "Fisher_directional", test_dir, c(1,1)), 'column names must be provided to scores and scores_direction')
   
   test_m <- test_matrix
   rownames(test_m) <- c("TP53", "GENE2", "GENE3")
   expect_error(merge_p_values(test_m, "Fisher_directional", test_direction_matrix, c(1,1)), 'scores_direction gene names must match scores genes')
   
   test_m <- test_matrix
   colnames(test_m) <- c("RNA","Mutation")
   expect_error(merge_p_values(test_m, "Fisher_directional", test_direction_matrix, c(1,1)),
                'scores_direction column names must match scores column names')
   
   expect_error(merge_p_values(test_matrix, "Fisher_directional", test_direction_matrix, c(1,1,-1)),
                'constraints_vector should have the same number of entries as columns in scores_direction')
   
   names(constraints_vector) <- c("Protein","RNA")
   expect_error(merge_p_values(test_matrix, "Fisher_directional", test_direction_matrix, constraints_vector),
                'the constraints_vector entries should match the order of scores and scores_direction columns')
})



test_that("P-value merging methods are correct", {
   expect_error(merge_p_values(c(0.05,0.10), "Fisher", c(1,1), c(1,1)),
                'Only DPM, Fisher_directional, Stouffer_directional, and Strube_directional methods support directional integration')
   
   expect_error(merge_p_values(c(0.05,0.10), "Tippett"),
                'Only Fisher, Brown, Stouffer and Strube methods are currently supported for non-directional analysis. 
             And only DPM, Fisher_directional, Stouffer_directional, and Strube_directional are supported for directional analysis')
   
   expect_error(merge_p_values(c(0.05,0.10), "Fisher_directional"),
                'scores_direction and constraints_vector must be provided for directional analyses')
   
})