tests/testthat/test-pivot-cna.R
In MSKCC-Epi-Bio/gnomeR: Wrangle and analyze IMPACT and TCGA mutation data
# Pivot Wider -----------------------------------------------------------------
test_that("pivot CNA- check amplification numbers", {
cna_long <- data.frame(
sampleId = c("P-0001276-T01-IM3","P-0001276-T01-IM3",
"P-0005436-T01-IM3",
"P-0001276-T01-IM3","P-0003333-T01-IM3"),
Hugo_Symbol = c("MLL2","KMT2D","HIST1H2BD",
"HIST1H3B","KDR"),
alteration = c("AMPLIFICATION","AMPLIFICATION",
"AMPLIFICATION","AMPLIFICATION","DELETION"))
expect_no_error(cna_wide <- pivot_cna_wider(cna_long))
nrow_long <- cna_long %>%
filter(sampleId == "P-0001276-T01-IM3" & alteration == "AMPLIFICATION") %>%
nrow(.)
len_wide <- length(cna_wide$`P-0001276-T01-IM3`[cna_wide$`P-0001276-T01-IM3` == 2])
expect_equal(nrow_long, len_wide)
})
test_that("pivot CNA- check ampl/del vs with 2/-1 alteration coding", {
cna_long_1 <- data.frame(
sampleId = c("P-0001276-T01-IM3","P-0001276-T01-IM3",
"P-0005436-T01-IM3",
"P-0001276-T01-IM3","P-0003333-T01-IM3"),
Hugo_Symbol = c("MLL2","KMT2D","HIST1H2BD",
"HIST1H3B","KDR"),
alteration = c("AMPLIFICATION","AMPLIFICATION",
"DELETION","AMPLIFICATION","DELETION"))
cna_wide_1 <- pivot_cna_wider(cna_long_1)
cna_long_2 <- data.frame(
sampleId = c("P-0001276-T01-IM3","P-0001276-T01-IM3",
"P-0005436-T01-IM3",
"P-0001276-T01-IM3","P-0003333-T01-IM3"),
Hugo_Symbol = c("MLL2","KMT2D","HIST1H2BD",
"HIST1H3B","KDR"),
alteration = c(2, 2, -2, 2, -2))
cna_wide_2 <- pivot_cna_wider(cna_long_2)
expect_equal(cna_wide_1, cna_wide_2)
cna_long_3 <- data.frame(
sampleId = c("P-0001276-T01-IM3","P-0001276-T01-IM3",
"P-0005436-T01-IM3",
"P-0001276-T01-IM3","P-0003333-T01-IM3"),
Hugo_Symbol = c("MLL2","KMT2D","HIST1H2BD",
"HIST1H3B","KDR"),
alteration = c("amplification","AMPLIFICATION",
"deletion","AMPLIFICATION","DELETION"))
cna_wide_3 <- pivot_cna_wider(cna_long_3)
expect_equal(cna_wide_3, cna_wide_2)
})
test_that("pivot CNA- check when NAs", {
cna_long_1 <- data.frame(
sampleId = c("P-0001276-T01-IM3","P-0001276-T01-IM3",
"P-0005436-T01-IM3",
"P-0001276-T01-IM3","P-0003333-T01-IM3"),
Hugo_Symbol = c("MLL2","KMT2D","HIST1H2BD",
"HIST1H3B","KDR"),
alteration = c(NA, "AMPLIFICATION",
"DELETION","AMPLIFICATION","DELETION"))
cna_wide_1 <- pivot_cna_wider(cna_long_1)
cna_long_2 <- data.frame(
sampleId = c("P-0001276-T01-IM3","P-0001276-T01-IM3",
"P-0005436-T01-IM3",
"P-0001276-T01-IM3","P-0003333-T01-IM3"),
Hugo_Symbol = c("MLL2","KMT2D","HIST1H2BD",
"HIST1H3B","KDR"),
alteration = c(NA, 2, -2, 2, -2))
cna_wide_2 <- pivot_cna_wider(cna_long_2)
expect_equal(cna_wide_1, cna_wide_2)
expect_equal(sum(is.na(cna_wide_2$`P-0001276-T01-IM3`)), 1)
expect_equal(sum(is.na(cna_wide_1$`P-0001276-T01-IM3`)), 1)
})
test_that("pivot CNA- unknown alteration vaues", {
cna_long_1 <- data.frame(
sampleId = c("P-0001276-T01-IM3","P-0001276-T01-IM3",
"P-0005436-T01-IM3",
"P-0001276-T01-IM3","P-0003333-T01-IM3"),
Hugo_Symbol = c("MLL2","KMT2D","HIST1H2BD",
"HIST1H3B","KDR"),
alteration = c(NA, "THING",
"OTHER_THING","AMPLIFICATION","DELETION"))
expect_error(pivot_cna_wider(cna_long_1), "Unknown values in alteration field:*")
})
test_that("pivot CNA- mixed coding in alteration column and 0/neutral", {
cna_long_1 <- data.frame(
sampleId = c("P-0001276-T01-IM3","P-0001276-T01-IM3",
"P-0005436-T01-IM3",
"P-0001276-T01-IM3","P-0003333-T01-IM3"),
Hugo_Symbol = c("MLL2","KMT2D","HIST1H2BD",
"HIST1H3B","KDR"),
alteration = c(NA, 2, 0, "AMPLIFICATION","DELETION"))
wide_cna_1 <- pivot_cna_wider(cna_long_1)
cna_long_2 <- data.frame(
sampleId = c("P-0001276-T01-IM3","P-0001276-T01-IM3",
"P-0005436-T01-IM3",
"P-0001276-T01-IM3","P-0003333-T01-IM3"),
Hugo_Symbol = c("MLL2","KMT2D","HIST1H2BD",
"HIST1H3B","KDR"),
alteration = c(NA, "AMPLIFICATION", "NEUTRAL", "AMPLIFICATION","DELETION"))
wide_cna_2 <- pivot_cna_wider(cna_long_2)
expect_equal(wide_cna_1, wide_cna_2)
})
test_that("pivot CNA- non standard sample IDs with periods", {
cna_long_1 <- data.frame(
sampleId = c("P.0001276.T01.IM3","P.0001276.T01.IM3",
"P.0005436.T01.IM3",
"P.0001276.T01.IM3","P.0003333.T01.IM3"),
Hugo_Symbol = c("MLL2","KMT2D","HIST1H2BD",
"HIST1H3B","KDR"),
alteration = c(NA, 2, 2, 1, -1))
expect_no_error(wide_cna_1 <- pivot_cna_wider(cna_long_1))
})
# Pivot Longer -----------------------------------------------------------------
test_that("pivot CNA- no CNA events error", {
cna_wide <- tibble::tribble(
~Hugo_Symbol, ~P.0070637.T01.IM7, ~P.0042589.T01.IM6, ~P.0026544.T01.IM6, ~P.0032011.T01.IM6,
"CRKL", 0L, 0L, 0L, 0L,
"SCG5", 0L, 0L, 0L, 0L,
"STK11", 0L, 0L, 0L, 0L,
"MEN1", 0L, 0L, 0L, 0L,
"B2M", 0L, 0L, 0L, 0L,
"TAP2", 0L, 0L, 0L, 0L,
"PMAIP1", 0L, 0L, 0L, 0L,
"H3-3A", 0L, 0L, 0L, 0L,
"H3-3B", 0L, 0L, 0L, 0L,
"CDC73", 0L, 0L, 0L, 0L,
"PIK3CA", 0L, 0L, 0L, 0L
)
expect_error(long_cna_1 <- pivot_cna_longer(cna_wide), "There are*")
})
test_that("pivot CNA- test clean_sample_ids = TRUE", {
cna_wide <- tibble::tribble(
~Hugo_Symbol, ~P.0070637.T01.IM7, ~P.0042589.T01.IM6, ~P.0026544.T01.IM6, ~P.0032011.T01.IM6,
"CRKL", 0L, 0L, 0L, -2L,
"SCG5", 0L, 0L, 0L, 0L,
"STK11", 1L, 0L, 0L, 0L,
"MEN1", 0L, 0L, 0L, 0L,
"B2M", 0L, 2L, 0L, 0L,
"TAP2", 0L, 0L, -1L, 0L,
"PMAIP1", 0L, 0L, 0L, 0L,
"H3-3A", 0L, 0L, 0L, 0L,
"H3-3B", 0L, 0L, 0L, 0L,
"CDC73", 0L, 0L, 0L, 0L,
"PIK3CA", 0L, 0L, 0L, -1L
)
expect_message(long_cna_1 <- pivot_cna_longer(cna_wide), "Replacing all*")
expect_false(any(str_detect(long_cna_1$sample_id, fixed("."))))
})
test_that("pivot CNA- test clean_sample_ids = FALSE", {
cna_wide <- tibble::tribble(
~Hugo_Symbol, ~P.0070637.T01.IM7, ~P.0042589.T01.IM6, ~P.0026544.T01.IM6, ~P.0032011.T01.IM6,
"CRKL", 0L, 0L, 0L, -2L,
"SCG5", 0L, 0L, 0L, 0L,
"STK11", 1L, 0L, 0L, 0L,
"MEN1", 0L, 0L, 0L, 0L,
"B2M", 0L, 2L, 0L, 0L,
"TAP2", 0L, 0L, -1L, 0L,
"PMAIP1", 0L, 0L, 0L, 0L,
"H3-3A", 0L, 0L, 0L, 0L,
"H3-3B", 0L, 0L, 0L, 0L,
"CDC73", 0L, 0L, 0L, 0L,
"PIK3CA", 0L, 0L, 0L, -1L
)
expect_no_message(long_cna_1 <- pivot_cna_longer(cna_wide, clean_sample_ids = FALSE))
expect_true(any(str_detect(long_cna_1$sample_id, fixed(".")))) })
test_that("pivot CNA- test patients with no events are not returned", {
cna_wide <- tibble::tribble(
~Hugo_Symbol, ~P.0070637.T01.IM7, ~P.0042589.T01.IM6, ~P.0026544.T01.IM6, ~P.0032011.T01.IM6,
"CRKL", 0L, 0L, 0L, -2L,
"SCG5", 0L, 0L, 0L, 0L,
"STK11", 1L, 0L, 0L, 0L,
"MEN1", 0L, 0L, 0L, 0L,
"B2M", 0L, 2L, 0L, 0L,
"TAP2", 0L, 0L, 0L, 0L,
"PMAIP1", 0L, 0L, 0L, 0L,
"H3-3A", 0L, 0L, 0L, 0L,
"H3-3B", 0L, 0L, 0L, 0L,
"CDC73", 0L, 0L, 0L, 0L,
"PIK3CA", 0L, 0L, 0L, -1L
)
no_hugo <- select(cna_wide, -Hugo_Symbol)
patient_sums <- apply(no_hugo, 2, function(x) sum(abs(x), na.rm = TRUE))
patient_with_cna <- patient_sums[patient_sums > 0] %>%
names()
cna_long <- pivot_cna_longer(cna_wide, clean_sample_ids = FALSE)
expect_equal(sort(unique(cna_long$sample_id)), sort(patient_with_cna))
})
test_that("pivot CNA- test number of CNA returned", {
cna_wide <- tibble::tribble(
~Hugo_Symbol, ~P.0070637.T01.IM7, ~P.0042589.T01.IM6, ~P.0026544.T01.IM6, ~P.0032011.T01.IM6,
"CRKL", 0L, 0L, 0L, -2L,
"SCG5", 0L, 0L, 0L, 0L,
"STK11", 1L, 0L, 0L, NA,
"MEN1", 0L, 0L, 0L, 0L,
"B2M", 0L, 2L, 0L, 0L,
"TAP2", 0L, 0L, 0L, 0L,
"PMAIP1", 0L, 0L, 0L, 0L,
"H3-3A", 0L, 0L, -1.5, 0L,
"H3-3B", 0L, 0L, 0L, 0L,
"CDC73", NA, 0L, 0L, 0L,
"PIK3CA", 0L, 0L, 0L, -1L
)
no_hugo <- dplyr::select(cna_wide, -Hugo_Symbol)
gene_table <- no_hugo %>%
tidyr::pivot_longer(everything()) %>%
unique() %>%
dplyr::filter(value != 0)
check <- case_when(
gene_table$value %in% c(-2, -1.5) ~ "deletion",
gene_table$value %in% c( -1) ~ "loss",
gene_table$value %in% c(2) ~ "amplification",
gene_table$value %in% c(1) ~ "gain")
cna_long <- pivot_cna_longer(cna_wide, clean_sample_ids = FALSE)
expect_equal(as.character(cna_long$alteration), check)
})
test_that("pivot CNA- test with NA data", {
cna_wide_zero <- tibble::tribble(
~Hugo_Symbol, ~P.0070637.T01.IM7, ~P.0042589.T01.IM6, ~P.0026544.T01.IM6, ~P.0032011.T01.IM6,
"CRKL", 0L, 0L, 0L, -2L,
"SCG5", 0L, 0L, 0L, 0L,
"STK11", 1L, 0L, 0L, 0L,
"MEN1", 0L, 0L, 0L, 0L,
"B2M", 0L, 2L, 0L, 0L,
"TAP2", 0L, 0L, 0L, 0L,
"PMAIP1", 0L, 0L, 0L, 0L,
"H3-3A", 0L, 0L, 0L, 0L,
"H3-3B", 0L, 0L, 0L, 0L,
"CDC73", 0L, 0L, 0L, 0L,
"PIK3CA", 0L, 0L, 0L, -1L
)
cna_wide_na <- tibble::tribble(
~Hugo_Symbol, ~P.0070637.T01.IM7, ~P.0042589.T01.IM6, ~P.0026544.T01.IM6, ~P.0032011.T01.IM6,
"CRKL", 0L, NA, 0L, -2L,
"SCG5", 0L, 0L, 0L, 0L,
"STK11", 1L, 0L, 0L, 0L,
"MEN1", 0L, 0L, 0L, 0L,
"B2M", 0L, 2L, 0L, 0L,
"TAP2", NA, 0L, 0L, 0L,
"PMAIP1", 0L, 0L, 0L, 0L,
"H3-3A", 0L, 0L, 0L, 0L,
"H3-3B", 0L, 0L, NA, 0L,
"CDC73", 0L, 0L, 0L, 0L,
"PIK3CA", 0L, 0L, 0L, -1L
)
expect_equal(pivot_cna_longer(cna_wide_zero, clean_sample_ids = FALSE),
pivot_cna_longer(cna_wide_na, clean_sample_ids = FALSE))
})
test_that("pivot CNA- test with character columns", {
cna_wide_na <- tibble::tribble(
~Hugo_Symbol, ~P.0070637.T01.IM7, ~P.0042589.T01.IM6, ~P.0026544.T01.IM6, ~P.0032011.T01.IM6,
"CRKL", 0L, NA, 0L, -2L,
"SCG5", 0L, 0L, 0L, 0L,
"STK11", 1L, 0L, 0L, 0L,
"MEN1", 0L, 0L, 0L, 0L,
"B2M", 0L, 2L, 0L, 0L,
"TAP2", NA, 0L, 0L, 0L,
"PMAIP1", 0L, 0L, 0L, 0L,
"H3-3A", 0L, 0L, 0L, 0L,
"H3-3B", 0L, 0L, NA, 0L,
"CDC73", 0L, 0L, 0L, 0L,
"PIK3CA", 0L, 0L, 0L, -1L
)
cna_wide_chr <- cna_wide_na %>%
mutate(across(.cols = c(everything(), -Hugo_Symbol), ~ as.character(.x)))
expect_error(pivot_cna_longer(cna_wide_chr, clean_sample_ids = FALSE))
})
test_that("pivot CNA- test with some character, some numeric columns", {
cna_wide_na <- tibble::tribble(
~Hugo_Symbol, ~P.0070637.T01.IM7, ~P.0042589.T01.IM6, ~P.0026544.T01.IM6, ~P.0032011.T01.IM6,
"CRKL", 0L, NA, 0L, -2L,
"SCG5", 0L, 0L, 0L, 0L,
"STK11", 1L, 0L, 0L, 0L,
"MEN1", 0L, 0L, 0L, 0L,
"B2M", 0L, 2L, 0L, 0L,
"TAP2", NA, 0L, 0L, 0L,
"PMAIP1", 0L, 0L, 0L, 0L,
"H3-3A", 0L, 0L, 0L, 0L,
"H3-3B", 0L, 0L, NA, 0L,
"CDC73", 0L, 0L, 0L, 0L,
"PIK3CA", 0L, 0L, 0L, -1L
)
cna_wide_chr <- cna_wide_na %>%
mutate(across(.cols = c(`P.0070637.T01.IM7`), ~ as.character(.x)))
expect_error(pivot_cna_longer(cna_wide_chr, clean_sample_ids = FALSE))
})
MSKCC-Epi-Bio/gnomeR documentation built on Oct. 17, 2024, 3:39 p.m.
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# Pivot Wider -----------------------------------------------------------------
test_that("pivot CNA- check amplification numbers", {
cna_long <- data.frame(
sampleId = c("P-0001276-T01-IM3","P-0001276-T01-IM3",
"P-0005436-T01-IM3",
"P-0001276-T01-IM3","P-0003333-T01-IM3"),
Hugo_Symbol = c("MLL2","KMT2D","HIST1H2BD",
"HIST1H3B","KDR"),
alteration = c("AMPLIFICATION","AMPLIFICATION",
"AMPLIFICATION","AMPLIFICATION","DELETION"))
expect_no_error(cna_wide <- pivot_cna_wider(cna_long))
nrow_long <- cna_long %>%
filter(sampleId == "P-0001276-T01-IM3" & alteration == "AMPLIFICATION") %>%
nrow(.)
len_wide <- length(cna_wide$`P-0001276-T01-IM3`[cna_wide$`P-0001276-T01-IM3` == 2])
expect_equal(nrow_long, len_wide)
})
test_that("pivot CNA- check ampl/del vs with 2/-1 alteration coding", {
cna_long_1 <- data.frame(
sampleId = c("P-0001276-T01-IM3","P-0001276-T01-IM3",
"P-0005436-T01-IM3",
"P-0001276-T01-IM3","P-0003333-T01-IM3"),
Hugo_Symbol = c("MLL2","KMT2D","HIST1H2BD",
"HIST1H3B","KDR"),
alteration = c("AMPLIFICATION","AMPLIFICATION",
"DELETION","AMPLIFICATION","DELETION"))
cna_wide_1 <- pivot_cna_wider(cna_long_1)
cna_long_2 <- data.frame(
sampleId = c("P-0001276-T01-IM3","P-0001276-T01-IM3",
"P-0005436-T01-IM3",
"P-0001276-T01-IM3","P-0003333-T01-IM3"),
Hugo_Symbol = c("MLL2","KMT2D","HIST1H2BD",
"HIST1H3B","KDR"),
alteration = c(2, 2, -2, 2, -2))
cna_wide_2 <- pivot_cna_wider(cna_long_2)
expect_equal(cna_wide_1, cna_wide_2)
cna_long_3 <- data.frame(
sampleId = c("P-0001276-T01-IM3","P-0001276-T01-IM3",
"P-0005436-T01-IM3",
"P-0001276-T01-IM3","P-0003333-T01-IM3"),
Hugo_Symbol = c("MLL2","KMT2D","HIST1H2BD",
"HIST1H3B","KDR"),
alteration = c("amplification","AMPLIFICATION",
"deletion","AMPLIFICATION","DELETION"))
cna_wide_3 <- pivot_cna_wider(cna_long_3)
expect_equal(cna_wide_3, cna_wide_2)
})
test_that("pivot CNA- check when NAs", {
cna_long_1 <- data.frame(
sampleId = c("P-0001276-T01-IM3","P-0001276-T01-IM3",
"P-0005436-T01-IM3",
"P-0001276-T01-IM3","P-0003333-T01-IM3"),
Hugo_Symbol = c("MLL2","KMT2D","HIST1H2BD",
"HIST1H3B","KDR"),
alteration = c(NA, "AMPLIFICATION",
"DELETION","AMPLIFICATION","DELETION"))
cna_wide_1 <- pivot_cna_wider(cna_long_1)
cna_long_2 <- data.frame(
sampleId = c("P-0001276-T01-IM3","P-0001276-T01-IM3",
"P-0005436-T01-IM3",
"P-0001276-T01-IM3","P-0003333-T01-IM3"),
Hugo_Symbol = c("MLL2","KMT2D","HIST1H2BD",
"HIST1H3B","KDR"),
alteration = c(NA, 2, -2, 2, -2))
cna_wide_2 <- pivot_cna_wider(cna_long_2)
expect_equal(cna_wide_1, cna_wide_2)
expect_equal(sum(is.na(cna_wide_2$`P-0001276-T01-IM3`)), 1)
expect_equal(sum(is.na(cna_wide_1$`P-0001276-T01-IM3`)), 1)
})
test_that("pivot CNA- unknown alteration vaues", {
cna_long_1 <- data.frame(
sampleId = c("P-0001276-T01-IM3","P-0001276-T01-IM3",
"P-0005436-T01-IM3",
"P-0001276-T01-IM3","P-0003333-T01-IM3"),
Hugo_Symbol = c("MLL2","KMT2D","HIST1H2BD",
"HIST1H3B","KDR"),
alteration = c(NA, "THING",
"OTHER_THING","AMPLIFICATION","DELETION"))
expect_error(pivot_cna_wider(cna_long_1), "Unknown values in alteration field:*")
})
test_that("pivot CNA- mixed coding in alteration column and 0/neutral", {
cna_long_1 <- data.frame(
sampleId = c("P-0001276-T01-IM3","P-0001276-T01-IM3",
"P-0005436-T01-IM3",
"P-0001276-T01-IM3","P-0003333-T01-IM3"),
Hugo_Symbol = c("MLL2","KMT2D","HIST1H2BD",
"HIST1H3B","KDR"),
alteration = c(NA, 2, 0, "AMPLIFICATION","DELETION"))
wide_cna_1 <- pivot_cna_wider(cna_long_1)
cna_long_2 <- data.frame(
sampleId = c("P-0001276-T01-IM3","P-0001276-T01-IM3",
"P-0005436-T01-IM3",
"P-0001276-T01-IM3","P-0003333-T01-IM3"),
Hugo_Symbol = c("MLL2","KMT2D","HIST1H2BD",
"HIST1H3B","KDR"),
alteration = c(NA, "AMPLIFICATION", "NEUTRAL", "AMPLIFICATION","DELETION"))
wide_cna_2 <- pivot_cna_wider(cna_long_2)
expect_equal(wide_cna_1, wide_cna_2)
})
test_that("pivot CNA- non standard sample IDs with periods", {
cna_long_1 <- data.frame(
sampleId = c("P.0001276.T01.IM3","P.0001276.T01.IM3",
"P.0005436.T01.IM3",
"P.0001276.T01.IM3","P.0003333.T01.IM3"),
Hugo_Symbol = c("MLL2","KMT2D","HIST1H2BD",
"HIST1H3B","KDR"),
alteration = c(NA, 2, 2, 1, -1))
expect_no_error(wide_cna_1 <- pivot_cna_wider(cna_long_1))
})
# Pivot Longer -----------------------------------------------------------------
test_that("pivot CNA- no CNA events error", {
cna_wide <- tibble::tribble(
~Hugo_Symbol, ~P.0070637.T01.IM7, ~P.0042589.T01.IM6, ~P.0026544.T01.IM6, ~P.0032011.T01.IM6,
"CRKL", 0L, 0L, 0L, 0L,
"SCG5", 0L, 0L, 0L, 0L,
"STK11", 0L, 0L, 0L, 0L,
"MEN1", 0L, 0L, 0L, 0L,
"B2M", 0L, 0L, 0L, 0L,
"TAP2", 0L, 0L, 0L, 0L,
"PMAIP1", 0L, 0L, 0L, 0L,
"H3-3A", 0L, 0L, 0L, 0L,
"H3-3B", 0L, 0L, 0L, 0L,
"CDC73", 0L, 0L, 0L, 0L,
"PIK3CA", 0L, 0L, 0L, 0L
)
expect_error(long_cna_1 <- pivot_cna_longer(cna_wide), "There are*")
})
test_that("pivot CNA- test clean_sample_ids = TRUE", {
cna_wide <- tibble::tribble(
~Hugo_Symbol, ~P.0070637.T01.IM7, ~P.0042589.T01.IM6, ~P.0026544.T01.IM6, ~P.0032011.T01.IM6,
"CRKL", 0L, 0L, 0L, -2L,
"SCG5", 0L, 0L, 0L, 0L,
"STK11", 1L, 0L, 0L, 0L,
"MEN1", 0L, 0L, 0L, 0L,
"B2M", 0L, 2L, 0L, 0L,
"TAP2", 0L, 0L, -1L, 0L,
"PMAIP1", 0L, 0L, 0L, 0L,
"H3-3A", 0L, 0L, 0L, 0L,
"H3-3B", 0L, 0L, 0L, 0L,
"CDC73", 0L, 0L, 0L, 0L,
"PIK3CA", 0L, 0L, 0L, -1L
)
expect_message(long_cna_1 <- pivot_cna_longer(cna_wide), "Replacing all*")
expect_false(any(str_detect(long_cna_1$sample_id, fixed("."))))
})
test_that("pivot CNA- test clean_sample_ids = FALSE", {
cna_wide <- tibble::tribble(
~Hugo_Symbol, ~P.0070637.T01.IM7, ~P.0042589.T01.IM6, ~P.0026544.T01.IM6, ~P.0032011.T01.IM6,
"CRKL", 0L, 0L, 0L, -2L,
"SCG5", 0L, 0L, 0L, 0L,
"STK11", 1L, 0L, 0L, 0L,
"MEN1", 0L, 0L, 0L, 0L,
"B2M", 0L, 2L, 0L, 0L,
"TAP2", 0L, 0L, -1L, 0L,
"PMAIP1", 0L, 0L, 0L, 0L,
"H3-3A", 0L, 0L, 0L, 0L,
"H3-3B", 0L, 0L, 0L, 0L,
"CDC73", 0L, 0L, 0L, 0L,
"PIK3CA", 0L, 0L, 0L, -1L
)
expect_no_message(long_cna_1 <- pivot_cna_longer(cna_wide, clean_sample_ids = FALSE))
expect_true(any(str_detect(long_cna_1$sample_id, fixed(".")))) })
test_that("pivot CNA- test patients with no events are not returned", {
cna_wide <- tibble::tribble(
~Hugo_Symbol, ~P.0070637.T01.IM7, ~P.0042589.T01.IM6, ~P.0026544.T01.IM6, ~P.0032011.T01.IM6,
"CRKL", 0L, 0L, 0L, -2L,
"SCG5", 0L, 0L, 0L, 0L,
"STK11", 1L, 0L, 0L, 0L,
"MEN1", 0L, 0L, 0L, 0L,
"B2M", 0L, 2L, 0L, 0L,
"TAP2", 0L, 0L, 0L, 0L,
"PMAIP1", 0L, 0L, 0L, 0L,
"H3-3A", 0L, 0L, 0L, 0L,
"H3-3B", 0L, 0L, 0L, 0L,
"CDC73", 0L, 0L, 0L, 0L,
"PIK3CA", 0L, 0L, 0L, -1L
)
no_hugo <- select(cna_wide, -Hugo_Symbol)
patient_sums <- apply(no_hugo, 2, function(x) sum(abs(x), na.rm = TRUE))
patient_with_cna <- patient_sums[patient_sums > 0] %>%
names()
cna_long <- pivot_cna_longer(cna_wide, clean_sample_ids = FALSE)
expect_equal(sort(unique(cna_long$sample_id)), sort(patient_with_cna))
})
test_that("pivot CNA- test number of CNA returned", {
cna_wide <- tibble::tribble(
~Hugo_Symbol, ~P.0070637.T01.IM7, ~P.0042589.T01.IM6, ~P.0026544.T01.IM6, ~P.0032011.T01.IM6,
"CRKL", 0L, 0L, 0L, -2L,
"SCG5", 0L, 0L, 0L, 0L,
"STK11", 1L, 0L, 0L, NA,
"MEN1", 0L, 0L, 0L, 0L,
"B2M", 0L, 2L, 0L, 0L,
"TAP2", 0L, 0L, 0L, 0L,
"PMAIP1", 0L, 0L, 0L, 0L,
"H3-3A", 0L, 0L, -1.5, 0L,
"H3-3B", 0L, 0L, 0L, 0L,
"CDC73", NA, 0L, 0L, 0L,
"PIK3CA", 0L, 0L, 0L, -1L
)
no_hugo <- dplyr::select(cna_wide, -Hugo_Symbol)
gene_table <- no_hugo %>%
tidyr::pivot_longer(everything()) %>%
unique() %>%
dplyr::filter(value != 0)
check <- case_when(
gene_table$value %in% c(-2, -1.5) ~ "deletion",
gene_table$value %in% c( -1) ~ "loss",
gene_table$value %in% c(2) ~ "amplification",
gene_table$value %in% c(1) ~ "gain")
cna_long <- pivot_cna_longer(cna_wide, clean_sample_ids = FALSE)
expect_equal(as.character(cna_long$alteration), check)
})
test_that("pivot CNA- test with NA data", {
cna_wide_zero <- tibble::tribble(
~Hugo_Symbol, ~P.0070637.T01.IM7, ~P.0042589.T01.IM6, ~P.0026544.T01.IM6, ~P.0032011.T01.IM6,
"CRKL", 0L, 0L, 0L, -2L,
"SCG5", 0L, 0L, 0L, 0L,
"STK11", 1L, 0L, 0L, 0L,
"MEN1", 0L, 0L, 0L, 0L,
"B2M", 0L, 2L, 0L, 0L,
"TAP2", 0L, 0L, 0L, 0L,
"PMAIP1", 0L, 0L, 0L, 0L,
"H3-3A", 0L, 0L, 0L, 0L,
"H3-3B", 0L, 0L, 0L, 0L,
"CDC73", 0L, 0L, 0L, 0L,
"PIK3CA", 0L, 0L, 0L, -1L
)
cna_wide_na <- tibble::tribble(
~Hugo_Symbol, ~P.0070637.T01.IM7, ~P.0042589.T01.IM6, ~P.0026544.T01.IM6, ~P.0032011.T01.IM6,
"CRKL", 0L, NA, 0L, -2L,
"SCG5", 0L, 0L, 0L, 0L,
"STK11", 1L, 0L, 0L, 0L,
"MEN1", 0L, 0L, 0L, 0L,
"B2M", 0L, 2L, 0L, 0L,
"TAP2", NA, 0L, 0L, 0L,
"PMAIP1", 0L, 0L, 0L, 0L,
"H3-3A", 0L, 0L, 0L, 0L,
"H3-3B", 0L, 0L, NA, 0L,
"CDC73", 0L, 0L, 0L, 0L,
"PIK3CA", 0L, 0L, 0L, -1L
)
expect_equal(pivot_cna_longer(cna_wide_zero, clean_sample_ids = FALSE),
pivot_cna_longer(cna_wide_na, clean_sample_ids = FALSE))
})
test_that("pivot CNA- test with character columns", {
cna_wide_na <- tibble::tribble(
~Hugo_Symbol, ~P.0070637.T01.IM7, ~P.0042589.T01.IM6, ~P.0026544.T01.IM6, ~P.0032011.T01.IM6,
"CRKL", 0L, NA, 0L, -2L,
"SCG5", 0L, 0L, 0L, 0L,
"STK11", 1L, 0L, 0L, 0L,
"MEN1", 0L, 0L, 0L, 0L,
"B2M", 0L, 2L, 0L, 0L,
"TAP2", NA, 0L, 0L, 0L,
"PMAIP1", 0L, 0L, 0L, 0L,
"H3-3A", 0L, 0L, 0L, 0L,
"H3-3B", 0L, 0L, NA, 0L,
"CDC73", 0L, 0L, 0L, 0L,
"PIK3CA", 0L, 0L, 0L, -1L
)
cna_wide_chr <- cna_wide_na %>%
mutate(across(.cols = c(everything(), -Hugo_Symbol), ~ as.character(.x)))
expect_error(pivot_cna_longer(cna_wide_chr, clean_sample_ids = FALSE))
})
test_that("pivot CNA- test with some character, some numeric columns", {
cna_wide_na <- tibble::tribble(
~Hugo_Symbol, ~P.0070637.T01.IM7, ~P.0042589.T01.IM6, ~P.0026544.T01.IM6, ~P.0032011.T01.IM6,
"CRKL", 0L, NA, 0L, -2L,
"SCG5", 0L, 0L, 0L, 0L,
"STK11", 1L, 0L, 0L, 0L,
"MEN1", 0L, 0L, 0L, 0L,
"B2M", 0L, 2L, 0L, 0L,
"TAP2", NA, 0L, 0L, 0L,
"PMAIP1", 0L, 0L, 0L, 0L,
"H3-3A", 0L, 0L, 0L, 0L,
"H3-3B", 0L, 0L, NA, 0L,
"CDC73", 0L, 0L, 0L, 0L,
"PIK3CA", 0L, 0L, 0L, -1L
)
cna_wide_chr <- cna_wide_na %>%
mutate(across(.cols = c(`P.0070637.T01.IM7`), ~ as.character(.x)))
expect_error(pivot_cna_longer(cna_wide_chr, clean_sample_ids = FALSE))
})
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