tests/testthat/test-recode_cna_alterations.R

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

# cna <- rename_columns(gnomeR::cna)
#
# cna_no_alt_long <- cna %>%
#   select(-alteration)
#
# not_allowed_nums <- cna %>%
#   mutate(alteration = 3)
#
# mixed_cna_labels <- cna %>%
#   select(-sample_id)%>% #changing alteration values so drop patient ID
#   mutate(alteration = c(1, rep("neutral", nrow(cna) - 1)))
#
#
# test_that("test no error thrown with example dataset", {
#   expect_error(.recode_cna_alterations(cna), NA)
#
#   alt_types <- names(table(.recode_cna_alterations(cna)$alteration))
#   expect_true("high level amplification" %in% alt_types)
#   expect_true("homozygous deletion" %in% alt_types)
#   expect_equal(length(alt_types), 2)
# })
#
#
# test_that("test what happens when api (wide) cna given", {
#   expect_error(.recode_cna_alterations(reformat_cna(cna)))
# })
#
#
# test_that("test that missing alteration throws error", {
#   expect_error(.recode_cna_alterations(cna_no_alt_long))
# })
#
# test_that("test that numbers < -2 or > 2 throw error", {
#   expect_error(.recode_cna_alterations(not_allowed_nums))
# })
#
# test_that("allowed to have numbers and characters in alteration column", {
#   expect_error(.recode_cna_alterations(mixed_cna_labels), NA)
#
#   mixed_cna_labels <- .recode_cna_alterations(mixed_cna_labels)
#
#   count_alterations <- mixed_cna_labels %>%
#     group_by(alteration)%>%
#     summarize(count = n())%>%
#     as.data.frame()
#
#   types_alterations <- names(table(mixed_cna_labels$alteration))
#
#
#   expect_equal(types_alterations, c("gain", "neutral"))
#   expect_equal(count_alterations[1, 2], 1) #only one gain
#   expect_equal(count_alterations[2, 2], nrow(mixed_cna_labels) - 1) #all others neutral
# })
#