Adding outstanding unit tests

tests/testthat/test-gene_ranger.R

@@ -0,0 +1,23 @@
+library(testthat)
+
+test_that("gene_ranger throws error with no genes", {
+  expect_error(gene_ranger())
+})
+
+test_that("gene_ranger throws error with invalid projection", {
+  expect_error(gene_ranger(these_genes = "MYC", projection = "invalid"))
+})
+
+test_that("gene_ranger throws error with invalid return format", {
+  expect_error(gene_ranger(these_genes = "MYC", return_as = "invalid"))
+})
+
+test_that("gene_ranger throws error when write_to_bed is TRUE but bed_path, track_name, or track_description is not provided", {
+  expect_error(gene_ranger(these_genes = "MYC", write_to_bed = TRUE), "Provide a path for output bed file")
+  expect_error(gene_ranger(these_genes = "MYC", write_to_bed = TRUE, bed_path = "my_bed"), "Provide a track name for output bed file")
+  expect_error(gene_ranger(these_genes = "MYC", write_to_bed = TRUE, bed_path = "my_bed", track_name = "MYC"), "Provide a track description for output bed file")
+})
+
+test_that("gene_ranger runs successfully with valid input", {
+  expect_silent(gene_ranger(these_genes = "MYC"))
+})

tests/testthat/test-purify_chr.R

@@ -0,0 +1,25 @@
+library(testthat)
+
+test_that("purify_chr throws error with no projection", {
+  expect_error(purify_chr(), "You must provide a valid projection")
+})
+
+test_that("purify_chr throws error with no incoming_table", {
+  expect_error(purify_chr(projection = "hg38"), "You must provide a data table with `incoming_table`")
+})
+
+test_that("purify_chr throws error with invalid projection", {
+  expect_error(purify_chr(projection = "invalid", incoming_table = data.frame(chrom = c("1", "2", "3"))), "This function supports the following projections")
+})
+
+test_that("purify_chr adds 'chr' prefix for hg38 projection", {
+  df = data.frame(chrom = c("1", "2", "3"))
+  result = purify_chr(projection = "hg38", incoming_table = df)
+  expect_equal(result$chrom, c("chr1", "chr2", "chr3"))
+})
+
+test_that("purify_chr removes 'chr' prefix for grch37 projection", {
+  df = data.frame(chrom = c("chr1", "chr2", "chr3"))
+  result = purify_chr(projection = "grch37", incoming_table = df)
+  expect_equal(result$chrom, c("1", "2", "3"))
+})

tests/testthat/test-purify_regions.R

@@ -0,0 +1,47 @@
+library(testthat)
+
+test_that("purify_regions handles single region string", {
+  result <- purify_regions(these_regions = "chr1:100-500")
+  expect_equal(nrow(result), 1)
+  expect_equal(result$chrom, "chr1")
+  expect_equal(result$start, 100)
+  expect_equal(result$end, 500)
+})
+
+test_that("purify_regions handles multiple region strings", {
+  result <- purify_regions(these_regions = c("chr1:100-500", "chr2:100-500"))
+  expect_equal(nrow(result), 2)
+  expect_equal(result$chrom, c("chr1", "chr2"))
+  expect_equal(result$start, c(100, 100))
+  expect_equal(result$end, c(500, 500))
+})
+
+test_that("purify_regions handles individual region parameters", {
+  result <- purify_regions(qchrom = "chr1", qstart = 100, qend = 500)
+  expect_equal(nrow(result), 1)
+  expect_equal(result$chrom, "chr1")
+  expect_equal(result$start, 100)
+  expect_equal(result$end, 500)
+})
+
+test_that("purify_regions handles multiple individual region parameters", {
+  result <- purify_regions(qchrom = c("chr1", "chr2"), qstart = c(100, 200), qend = c(500, 600))
+  expect_equal(nrow(result), 2)
+  expect_equal(result$chrom, c("chr1", "chr2"))
+  expect_equal(result$start, c(100, 200))
+  expect_equal(result$end, c(500, 600))
+})
+
+test_that("purify_regions handles data frame input", {
+  my_regions <- data.frame(chrom = c("chr1", "chr2"), start = c(100, 200), end = c(500, 600))
+  result <- purify_regions(these_regions = my_regions)
+  expect_equal(nrow(result), 2)
+  expect_equal(result$chrom, c("chr1", "chr2"))
+  expect_equal(result$start, c(100, 200))
+  expect_equal(result$end, c(500, 600))
+})
+
+test_that("purify_regions throws error with incorrect input", {
+  expect_error(purify_regions(qchrom = "chr1", qstart = 100))
+  expect_error(purify_regions(these_regions = data.frame(chrom = c("chr1", "chr2"), start = c(100, 200), end = c(50, 100))))
+})

tests/testthat/test-region_ranger.R

@@ -0,0 +1,23 @@
+library(testthat)
+
+test_that("region_ranger throws error with no regions", {
+  expect_error(region_ranger())
+})
+
+test_that("region_ranger throws error with invalid projection", {
+  expect_error(region_ranger(these_regions = "chr8:127735434-127742951", projection = "invalid"), "This function supports the following projections")
+})
+
+test_that("region_ranger returns correct number of columns when raw is FALSE", {
+  result = region_ranger(these_regions = "chr8:127735434-127742951")
+  expect_equal(ncol(result), 11)
+})
+
+test_that("region_ranger returns all columns when raw is TRUE", {
+  result = region_ranger(these_regions = "chr8:127735434-127742951", raw = TRUE)
+  expect_true(ncol(result) > 11)
+})
+
+test_that("region_ranger returns warning when no genes found", {
+  expect_warning(region_ranger(these_regions = "chr1:1-10"))
+})

tests/testthat/test-sanity_check_regions.R

@@ -0,0 +1,31 @@
+library(testthat)
+
+test_that("sanity_check_regions throws error with no regions", {
+  expect_error(sanity_check_regions(), "No regions provided")
+})
+
+test_that("sanity_check_regions throws error with invalid projection", {
+  my_regions <- data.frame(chrom = c("chr1"), start = c(100), end = c(200))
+  expect_error(sanity_check_regions(incoming_regions = my_regions, projection = "invalid"), "Invalid projection specified")
+})
+
+test_that("sanity_check_regions throws error when start is greater than end", {
+  my_regions <- data.frame(chrom = c("chr1"), start = c(200), end = c(100))
+  expect_error(sanity_check_regions(incoming_regions = my_regions, projection = "hg38"), "start is greater than or equal to end")
+})
+
+test_that("sanity_check_regions throws error when start or end is outside chromosomal range", {
+  my_regions <- data.frame(chrom = c("chr1"), start = c(100), end = c(300000000))
+  expect_error(sanity_check_regions(incoming_regions = my_regions, projection = "hg38"), "Specified start or end coordinates fall outside the actual chromosomal range")
+})
+
+test_that("sanity_check_regions runs successfully with valid input", {
+  my_regions <- data.frame(chrom = c("chr1"), start = c(100), end = c(200))
+  expect_silent(sanity_check_regions(incoming_regions = my_regions, projection = "hg38"))
+})
+
+test_that("sanity_check_regions runs successfully with valid input", {
+  my_regions <- data.frame(chrom = c("1"), start = c(100), end = c(200))
+  expect_silent(sanity_check_regions(incoming_regions = my_regions, projection = "grch37"))
+})
+