tests/testthat/test-sanitize.R

In MSKCC-Epi-Bio/gnomeR: Wrangle and analyze IMPACT and TCGA mutation data

#
# # General Test ----------------------------------------------------------------
# test_that("both sanitize functions run with no errors", {
#   mut <- rename_columns(gnomeR::mutations)
#   sv <- rename_columns(sv)
#
#   expect_error(.sanitize_mutation_input(mut, include_silent = FALSE), NA)
#   expect_error(.sanitize_mutation_input(mut, include_silent = TRUE), NA)
#   expect_error(.sanitize_fusion_input(sv), NA)
# })
#
#
# test_that("test to see what happens if pass sanitize a vector", {
#   mut <- rename_columns(gnomeR::mutations)
#   sv <- rename_columns(sv)
#
#   expect_error(.sanitize_mutation_input(gnomeR::mutations %>%
#                                            select(-Hugo_Symbol),
#                                        include_silent = FALSE))
#   expect_error(.sanitize_fusion_input(gnomeR::sv %>%
#                                          select(-Hugo_Symbol)))
# })
#
# test_that("alterations properly recoded using internal func", {
#   cna <- gnomeR::cna[1:10,]%>%
#     rename_columns() %>%
#     .sanitize_cna_input()
#
#   expect_true("amplification" %in% names(table(cna$alteration)))
#   expect_true("deletion" %in% names(table(cna$alteration)))
#
#   table <- as.data.frame(table(cna$alteration))
#
#   expect_equal(table$Freq[table$Var1 == "deletion"], 7)
#   expect_equal(table$Freq[table$Var1 == "amplification"], 3)
# })
#
#
# # --------------------------------------------------------------
# # Test fusion in variant classification
#
# test_that("test fusion in variant classification", {
#   mutation = gnomeR::mutations
#   mutation <- rename_columns(mutation)
#   column_names <- colnames(mutation)
#   mutation$variant_classification[mutation$variant_classification == "In_Frame_Del"] <- "fusion"
#
#   expect_error(.sanitize_mutation_input(mutation, include_silent = F), "It looks like you have fusions in your mutation data frame.*")
# })
#
#
# test_that("test fusion in variant classification", {
#   mutation = gnomeR::mutations
#   mutation <- rename_columns(mutation)
#   column_names <- colnames(mutation)
#   mutation = mutation %>% select(-mutation_status)
#
#   expect_warning(.sanitize_mutation_input(mutation, include_silent = F), "A mutation_status column*")
#
#   mutation = mutation %>%
#     mutate(mutation_status = "SOMATIC")
#
#   expect_no_error(.sanitize_mutation_input(mutation, include_silent = F))
# })
#
# # variant type
#
# test_that("test variant type", {
#   mutation = gnomeR::mutations
#   mutation <- rename_columns(mutation)
#   column_names <- colnames(mutation)
#   mutation = mutation %>% select(-c(variant_type, reference_allele))
#
#   expect_error(.sanitize_mutation_input(mutation, include_silent = F))
# })
#
# test_that("test variant type inference", {
#   mutation = gnomeR::mutations
#   mutation <- rename_columns(mutation)
#   column_names <- colnames(mutation)
#   mutation = mutation %>% select(-c(variant_type))
#   mutation$tumor_seq_allele_2 = mutation$reference_allele
#
#   expect_warning(.sanitize_mutation_input(mutation, include_silent = F))
# })
#
#
# test_that("test variant type inference error", {
#   mutation = gnomeR::mutations
#   mutation <- rename_columns(mutation)
#   column_names <- colnames(mutation)
#   mutation$tumor_seq_allele_2 = mutation$reference_allele
#   mutation = mutation %>% select(-c(variant_type, reference_allele))
#
#   expect_error(.sanitize_mutation_input(mutation, include_silent = F))
# })
#
#
# test_that("test that attributes are returned for input data col names", {
#
#   mutation <- sanitize_mutation_input(gnomeR::mutations, include_silent = F)
#   expect_true(!is.null(attr(mutation, "names_dict")))
#
#   cna <- sanitize_cna_input(gnomeR::cna)
#   expect_true(!is.null(attr(cna, "names_dict")))
#
#   fus <- sanitize_fusion_input(gnomeR::sv)
#   expect_true(!is.null(attr(fus, "names_dict")))
#
#
# })
#
#
#
# test_that("Check input colname is used in messaging", {
#
#   mut_maf <- gnomeR::mutations %>%
#     select(-variantType) %>%
#     mutate(Tumor_Seq_Allele2 = NA)
#
#   x <- capture_warning(sanitize_mutation_input(mut_maf, include_silent = FALSE))
#   expect_true(str_detect(x$message, "Tumor_Seq_Allele2"))
#
#
# })
#
#
# # Test Specific Utils -----------------------------------------------------
#
# test_that("clean and check columns works and cleans names", {
#
#   expect_no_error(
#     res <- .clean_and_check_cols(df_to_check = gnomeR::mutations))
#
#   expect_true("hugo_symbol" %in% names(res))
# })
#
# test_that("clean and check columns returns character vectors", {
#
#   mut <- gnomeR::mutations[1:10, ]
#   mut$sampleId <- as.factor(mut$sampleId)
#
#   expect_no_error(
#     res <- .clean_and_check_cols(df_to_check = mut))
#
#   expect_equal(class(res$sample_id), "character")
#
# })
#
# test_that("test check required cols works", {
#   expect_no_error(.check_required_cols(rename_columns(gnomeR::mutations),
#                        required_cols = c("sample_id", "hugo_symbol")))
#
# })
#
# test_that("test check required cols throws error when missing", {
#
#   mut <- gnomeR::mutations %>%
#     rename("sample_id" = sampleId) %>%
#     select(-sample_id)
#
#   expect_error(
#     .check_required_cols(mut, required_cols = c("sample_id", "hugo_symbol"))
#     )
#
# })
#
#