Nothing
tests/testthat/test-genomics-by-sample.R
In cbioportalR: Browse and Query Clinical and Genomic Data from cBioPortal
# Tests core `.get_data_by_sample` (and genomics-specific tests) -----------------
test_that("Test study_id and Profile Param", {
skip_on_cran()
skip_if(httr::http_error("www.cbioportal.org/api"))
# > expand.grid(study_id = c("correct", "incorrect", "NULL"),
# profile = c("correct", "incorrect", "NULL"))
#
# study_id profile
# 1 correct correct
# 2 incorrect correct
# 3 NULL correct
# 4 correct incorrect
# 5 incorrect incorrect
# 6 NULL incorrect
# 7 correct NULL
# 8 incorrect NULL
# 9 NULL NULL
db_test <- "public"
set_cbioportal_db(db = db_test)
data_type = "mutation"
# Parameter Tests ------------
# study_id = correct, profile = correct ~ WORKS
expect_message(.get_data_by_sample(
study_id = "acc_tcga",
molecular_profile_id = "acc_tcga_mutations",
sample_id = c("TCGA-OR-A5J2-01","TCGA-OR-A5J6-01"),
data_type = data_type), "*")
# HERE
# study_id = incorrect, profile = correct ~ Throw message ignoring study_id
expect_message(.get_data_by_sample(
study_id = "not_here",
molecular_profile_id = "acc_tcga_mutations",
sample_id = c("TCGA-OR-A5J2-01","TCGA-OR-A5J6-01"),
data_type = data_type), "You have passed*")
# study_id = NULL, profile = correct - WORKS - guesses study ID
expect_error(.get_data_by_sample(
study_id = NULL,
molecular_profile_id = "acc_tcga_mutations",
sample_id = c("TCGA-OR-A5J2-01","TCGA-OR-A5J6-01"),
data_type = data_type), NA)
# study_id = correct, profile = incorrect -FAIL Informative Error
expect_error(.get_data_by_sample(
study_id = "acc_tcga",
molecular_profile_id = "nope",
sample_id = c("TCGA-OR-A5J2-01","TCGA-OR-A5J6-01"),
data_type = data_type), "Molecular*")
#study_id = incorrect, profiles = incorrect - gives informative error
expect_error(.get_data_by_sample(
study_id = "blah",
molecular_profile_id = "wrong",
sample_id = c("TCGA-OR-A5J2-01","TCGA-OR-A5J6-01"),
data_type = data_type), "Molecular profile*")
# study ID = correct, profile = NULL - gives informative error
expect_error(.get_data_by_sample(
study_id = NULL,
molecular_profile_id = "blah",
sample_id = c("TCGA-OR-A5J2-01","TCGA-OR-A5J6-01"),
data_type = data_type), "Molecular*")
# study ID = correct, profile = NULL -WORKS- looks up profile ID
expect_error(.get_data_by_sample(
study_id = "acc_tcga",
molecular_profile_id = NULL,
sample_id = c("TCGA-OR-A5J2-01","TCGA-OR-A5J6-01"),
data_type = data_type), NA)
# study_id = incorrect, profile = NULL **API fail error (could be more informative)
expect_error(.get_data_by_sample(
study_id = "not_here",
molecular_profile_id = NULL,
sample_id = c("TCGA-OR-A5J2-01","TCGA-OR-A5J6-01"),
data_type = data_type), "API*")
# study_id = NULL, profile = NULL ~ uses default study
expect_error(.get_data_by_sample(
study_id = NULL,
molecular_profile_id = NULL,
sample_id = c("TCGA-OR-A5J2-01","TCGA-OR-A5J6-01"),
data_type = data_type), NA)
# Other-------------
# no sample IDs passed
expect_error(.get_data_by_sample(
study_id = "acc_tcga",
molecular_profile_id = NULL,
data_type = data_type), "You must pass*")
# study_id > 1 passed
expect_error(.get_data_by_sample(
study_id = c("acc_tcga", "tt"),
sample_id = c("TCGA-OR-A5J2-01","TCGA-OR-A5J6-01"),
molecular_profile_id = NULL,
data_type = data_type), "More*")
# both correct, but bad base URL
expect_error(.get_data_by_sample(study_id = "acc_tcga",
molecular_profile_id = "acc_tcga_mutations",
sample_id = c("TCGA-OR-A5J2-01","TCGA-OR-A5J6-01"),
data_type = data_type, base_url = "plunk"), "API*")
# both exist but mismatched- ignores study ID but works
expect_error(.get_data_by_sample(study_id = "acc_tcga",
molecular_profile_id = "mpnst_mskcc_mutations",
sample_id = c("TCGA-OR-A5J2-01","TCGA-OR-A5J6-01"),
data_type = data_type), NA)
# fusions don't exist
expect_error(.get_data_by_sample(
study_id = "acc_tcga",
sample_id = c("TCGA-OR-A5J2-01","TCGA-OR-A5J6-01"),
molecular_profile_id = "acc_tcga_structural_variants", data_type = "fusion"), "Molecular profile*")
})
test_that("Test sample-study pairs df", {
skip_on_cran()
skip_if(httr::http_error("www.cbioportal.org/api"))
db_test <- "public"
set_cbioportal_db(db = db_test)
data_type = "mutation"
# works ---
df_pairs <- data.frame(
"sample_id" = c("P-0002146-T01-IM3", "s_C_CAUWT7_P001_d"),
"study_id" = c("blca_plasmacytoid_mskcc_2016", "prad_msk_2019"))
expect_error(.get_data_by_sample(sample_study_pairs = df_pairs,
data_type = data_type), NA)
# doesn't work (for now) ---
df_pairs <- data.frame(
"sample_id" = c("P-0002146-T01-IM3", "s_C_CAUWT7_P001_d"),
"molecular_profile_id" = c("blca_plasmacytoid_mskcc_2016_mutations", "prad_msk_2019_mutations"))
expect_error(.get_data_by_sample(sample_study_pairs = df_pairs,
data_type = "fusion"), "*")
# need colnames ---
df_pairs <- data.frame(
"wrong" = c("P-0002146-T01-IM3", "s_C_CAUWT7_P001_d"),
"study_id" = c("blca_plasmacytoid_mskcc_2016", "prad_msk_2019"))
expect_error(.get_data_by_sample(sample_study_pairs = df_pairs,
data_type = data_type), "*")
# need colnames ---
df_pairs <- data.frame(
"sample_id" = c("P-0002146-T01-IM3", "s_C_CAUWT7_P001_d"),
"wrong" = c("blca_plasmacytoid_mskcc_2016", "prad_msk_2019"))
expect_error(.get_data_by_sample(sample_study_pairs = df_pairs,
data_type = data_type), "*")
# approximate colnames work ---
sample_study_pairs <- data.frame(
"SAMPLE ID" = c("P-0002146-T01-IM3", "s_C_CAUWT7_P001_d"),
"studyID" = c("blca_plasmacytoid_mskcc_2016", "prad_msk_2019"),
"moLEcularProfile ID" = c("blca_plasmacytoid_mskcc_2016_mutations", "prad_msk_2019_mutations"))
expect_error(.get_data_by_sample(sample_study_pairs = sample_study_pairs,
data_type = data_type), NA)
#additional columns ignored ---
sample_study_pairs <- data.frame(
"SAMPLE ID" = c("P-0002146-T01-IM3", "s_C_CAUWT7_P001_d"),
"studyID" = c("blca_plasmacytoid_mskcc_2016", "prad_msk_2019"),
"moLEcularProfile ID" = c("blca_plasmacytoid_mskcc_2016_mutations", "prad_msk_2019_mutations"),
"rando" = c("h", "i"))
expect_error(.get_data_by_sample(sample_study_pairs = sample_study_pairs,
data_type = data_type), NA)
})
test_that("data is same regardless of function", {
skip_on_cran()
skip_if(httr::http_error("www.cbioportal.org/api"))
db_test <- "public"
set_cbioportal_db(db = db_test)
sample_id = c("s_C_03LNU8_P001_d", "s_C_36924L_P001_d", "s_C_CAUWT7_P001_d")
# molecular_profile_id = "mpnst_mskcc_mutations"
study_id = "prad_msk_2019"
get_gen <- get_genetics_by_sample(sample_id = sample_id,
study_id = study_id)
# Mutation
molecular_profile_id = "prad_msk_2019_mutations"
by_study <- get_mutations_by_sample(sample_id = sample_id, study_id = study_id)
by_prof <- get_mutations_by_sample(sample_id = sample_id, molecular_profile_id = molecular_profile_id)
expect_identical(by_study, by_prof, get_gen$mutation)
# CNA ---
molecular_profile_id = "prad_msk_2019_cna"
by_study <- get_cna_by_sample(sample_id = sample_id, study_id = study_id)
by_prof <- get_cna_by_sample(sample_id = sample_id, molecular_profile_id = molecular_profile_id)
expect_identical(by_study, by_prof, get_gen$cna)
# Fusions ---
molecular_profile_id = "prad_msk_2019_structural_variants"
by_study <- get_fusions_by_sample(sample_id = sample_id, study_id = study_id)
by_study2 <- get_structural_variants_by_sample(sample_id = sample_id, study_id = study_id)
by_prof <- get_fusions_by_sample(sample_id = sample_id, molecular_profile_id = molecular_profile_id)
by_prof2 <- get_structural_variants_by_sample(sample_id = sample_id, molecular_profile_id = molecular_profile_id)
expect_identical(by_study, by_study2, by_prof, by_prof2, get_gen$structural_variant)
})
test_that("Unknown Hugo Symbol returns Unk ", {
skip_on_cran()
skip_if(httr::http_error("www.cbioportal.org/api"))
set_cbioportal_db("public")
df <- get_cna_by_sample(sample_id =c("TCGA-OR-A5J2-01","TCGA-OR-A5J6-01"),
study_id = "acc_tcga")
df[16, ] <- df[15,]
df[16, 'entrezGeneId'] <- 1000000
df <- df %>% select(-"hugoGeneSymbol")
df2 <- .lookup_hugo(df)
expect_true(any(stringr::str_detect(df2$hugoGeneSymbol, "unk")))
})
test_that("Hugo Symbol is added by default", {
skip_on_cran()
skip_if(httr::http_error("www.cbioportal.org/api"))
set_cbioportal_db("public")
df <- get_genetics_by_sample(sample_id =c("TCGA-OR-A5J2-01","TCGA-OR-A5J6-01"),
study_id = "acc_tcga")
expect_true(length(df$mutation$hugoGeneSymbol) > 1)
expect_true(length(df$cna$hugoGeneSymbol) > 1)
})
test_that("`add_hugo` = FALSE doesn't add column if it's not there", {
skip_on_cran()
skip_if(httr::http_error("www.cbioportal.org/api"))
set_cbioportal_db("public")
df_hugo_false <- get_genetics_by_sample(sample_id =c("s_C_CAUWT7_P001_d",
"s_C_DU6ECC_P002_d",
"s_C_M8X42T_P002_d",
"s_C_36924L_P001_d"),
study_id = "prad_msk_2019", add_hugo = FALSE)
df_hugo_true <- get_genetics_by_sample(sample_id =c("s_C_CAUWT7_P001_d",
"s_C_DU6ECC_P002_d",
"s_C_M8X42T_P002_d",
"s_C_36924L_P001_d"),
study_id = "prad_msk_2019", add_hugo = TRUE)
expect_true(setdiff(names(df_hugo_true$mutation), names(df_hugo_false$mutation)) == "hugoGeneSymbol")
expect_true(setdiff(names(df_hugo_true$cna), names(df_hugo_false$cna)) == "hugoGeneSymbol")
expect_true(length(setdiff(names(df_hugo_true$structural_variant), names(df_hugo_false$structural_variant))) == 0)
})
test_that("`add_hugo= TRUE` warns if column already exists", {
skip_on_cran()
skip_if(httr::http_error("www.cbioportal.org/api"))
set_cbioportal_db("public")
df <- get_genetics_by_sample(sample_id =c("TCGA-OR-A5J2-01","TCGA-OR-A5J6-01"),
study_id = "acc_tcga")
expect_warning(.lookup_hugo(df$mutation), "*")
})
test_that("Returns same results as pulling by study ID ", {
skip_on_cran()
skip_if(httr::http_error("www.cbioportal.org/api"))
set_cbioportal_db("public")
all <- available_samples("blca_plasmacytoid_mskcc_2016")
resolved_genes <- cbioportalR::impact_gene_info$entrez_id %>% unlist()
x <- .get_data_by_sample(sample_id = all$sampleId,
study_id = "blca_plasmacytoid_mskcc_2016", data_type = "cna")
y <-.get_data_by_sample(sample_id = all$sampleId,
study_id = "blca_plasmacytoid_mskcc_2016", data_type = "cna")
resolved_genes <- cbioportalR::impact_gene_info$entrez_id %>% unlist()
z <-.get_data_by_sample(sample_id = all$sampleId,
study_id = "blca_plasmacytoid_mskcc_2016", data_type = "cna",
genes = resolved_genes)
expect_true(length(setdiff(x$hugoGeneSymbol, z$hugoGeneSymbol)) != 0)
})
test_that("test entrez ID to hugo symbol in get_xx_by_sample functions", {
skip_on_cran()
skip_if(httr::http_error("www.cbioportal.org/api"))
set_cbioportal_db("public")
# get all genes returned for this study
all_genes <- get_genetics_by_study(study_id = "blca_plasmacytoid_mskcc_2016")
# try to pull genetics by sample using entrez IDs
# get study ID-sample ID pairs
s1 <- available_samples("blca_plasmacytoid_mskcc_2016") %>%
transmute(sample_id = sampleId, study_id = studyId)
all_genomic_entrez <- get_genetics_by_sample(sample_study_pairs = s1,
genes = all_genes$mutation$entrezGeneId)
# convert relevant entrez IDs to hugo symbols
entrez_to_hugo <- get_hugo_symbol(all_genes$mutation$entrezGeneId)
# try to pull genetics by sample using the converted Hugo symbols
all_genomic_hugo <- get_genetics_by_sample(sample_study_pairs = s1,
genes = entrez_to_hugo$hugoGeneSymbol)
expect_equal(all_genomic_entrez$mutation, all_genomic_hugo$mutation)
expect_equal(all_genomic_entrez$cna, all_genomic_hugo$cna)
expect_equal(all_genomic_entrez$structural_variant, all_genomic_hugo$structural_variant)
})
test_that("pulling with gene ID (entrez or hugo) works with no error", {
skip_on_cran()
skip_if(httr::http_error("www.cbioportal.org/api"))
set_cbioportal_db("public")
genes = get_entrez_id(c("ERBB2", "PIK3C2G",
"CDKN1A", "EPHA2", "NOTCH2"))
s1 <- available_samples("blca_plasmacytoid_mskcc_2016") %>%
transmute(sample_id = sampleId, study_id = studyId)
gen_by_entrez <- get_genetics_by_sample(sample_study_pairs = s1,
genes = genes$entrezGeneId)
gen_by_hugo <- get_genetics_by_sample(sample_study_pairs = s1,
genes = genes$hugoGeneSymbol)
expect_true(identical(gen_by_entrez$mutation, gen_by_hugo$mutation))
expect_true(identical(gen_by_entrez$cna, gen_by_hugo$cna))
expect_true(identical(gen_by_entrez$structural_variant, gen_by_hugo$structural_variant))
})
test_that("pulling with panel ID works with no error and matches pull by gene", {
skip_on_cran()
skip_if(httr::http_error("www.cbioportal.org/api"))
set_cbioportal_db("public")
s1 <- available_samples("blca_plasmacytoid_mskcc_2016") %>%
transmute(sample_id = sampleId, study_id = studyId)
expect_error(gen_by_panel <- get_genetics_by_sample(sample_study_pairs = s1,
panel = "IMPACT468"), NA)
genes <- get_gene_panel("IMPACT468")
gen_by_entrez <- get_genetics_by_sample(sample_study_pairs = s1,
genes = genes$entrezGeneId)
expect_true(identical(gen_by_panel$mutation, gen_by_entrez$mutation))
expect_true(identical(gen_by_panel$cna, gen_by_entrez$cna))
expect_true(identical(gen_by_panel$structural_variant, gen_by_entrez$structural_variant))
})
test_that("pulling with panel ID works with no error and matches pull by gene", {
skip_on_cran()
skip_if(httr::http_error("www.cbioportal.org/api"))
set_cbioportal_db("public")
s1 <- available_samples("blca_plasmacytoid_mskcc_2016") %>%
dplyr::transmute(sample_id = sampleId, study_id = studyId)
# error if misspecified panel
expect_error(get_mutations_by_sample(sample_study_pairs = s1,
panel = "ttt"), "*")
# no error if correct panel
expect_error(gen_by_panel <- get_genetics_by_sample(sample_study_pairs = s1,
panel = "IMPACT468"), NA)
genes <- get_gene_panel("IMPACT468")
gen_by_entrez <- get_genetics_by_sample(sample_study_pairs = s1,
genes = genes$entrezGeneId)
expect_true(identical(gen_by_panel$mutation, gen_by_entrez$mutation))
expect_true(identical(gen_by_panel$cna, gen_by_entrez$cna))
expect_true(identical(gen_by_panel$structural_variant, gen_by_entrez$structural_variant))
})
test_that("pull by panel ID + gene IDs", {
skip_on_cran()
skip_if(httr::http_error("www.cbioportal.org/api"))
set_cbioportal_db("public")
s1 <- available_samples("blca_plasmacytoid_mskcc_2016") %>%
dplyr::transmute(sample_id = sampleId, study_id = studyId)
plus_gene <- "NOTCH4"
plus_entrez = get_entrez_id(plus_gene)$entrezGeneId
expect_error(gen_by_panel <- get_genetics_by_sample(sample_study_pairs = s1,
panel = "sarc_mskcc_panel", genes = plus_gene), NA)
expect_error(gen_by_panel2 <- get_genetics_by_sample(sample_study_pairs = s1,
panel = "sarc_mskcc_panel", genes = plus_entrez), NA)
expect_error(gen_by_panel3 <- get_genetics_by_sample(sample_study_pairs = s1,
panel = "sarc_mskcc_panel"), NA)
expect_true(identical(gen_by_panel$mutation, gen_by_panel2$mutation))
expect_true(identical(gen_by_panel$cna, gen_by_panel2$cna))
expect_true(identical(gen_by_panel$structural_variant, gen_by_panel2$structural_variant))
expect_equal(setdiff(gen_by_panel$mutation$hugoGeneSymbol,
gen_by_panel3$mutation$hugoGeneSymbol), plus_gene)
})
test_that("pull by two panel IDs", {
skip_on_cran()
skip_if(httr::http_error("www.cbioportal.org/api"))
set_cbioportal_db("public")
s1 <- c("DS-sig-010-P2", "DS-sig-010-P1", "DS-sig-018-P")
panels <- c("IMPACT468", "sarc_mskcc_panel")
ids <- get_gene_panel(panels) %>%
dplyr::pull(entrezGeneId) %>%
unique()
expect_error(gen_by_panel <- get_mutations_by_sample(sample_id = s1,
study_id = "blca_plasmacytoid_mskcc_2016",
panel = c("IMPACT468", "sarc_mskcc_panel"),
genes = "NOTCH2"), NA)
expect_error(gen_by_panel2 <- get_mutations_by_sample(sample_id = s1,
study_id = "blca_plasmacytoid_mskcc_2016",
panel = c("sarc_mskcc_panel"),
genes = "NOTCH2"), NA)
expect_true(length(gen_by_panel$hugoGeneSymbol) > length(gen_by_panel2$hugoGeneSymbol))
})
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# Tests core `.get_data_by_sample` (and genomics-specific tests) -----------------
test_that("Test study_id and Profile Param", {
skip_on_cran()
skip_if(httr::http_error("www.cbioportal.org/api"))
# > expand.grid(study_id = c("correct", "incorrect", "NULL"),
# profile = c("correct", "incorrect", "NULL"))
#
# study_id profile
# 1 correct correct
# 2 incorrect correct
# 3 NULL correct
# 4 correct incorrect
# 5 incorrect incorrect
# 6 NULL incorrect
# 7 correct NULL
# 8 incorrect NULL
# 9 NULL NULL
db_test <- "public"
set_cbioportal_db(db = db_test)
data_type = "mutation"
# Parameter Tests ------------
# study_id = correct, profile = correct ~ WORKS
expect_message(.get_data_by_sample(
study_id = "acc_tcga",
molecular_profile_id = "acc_tcga_mutations",
sample_id = c("TCGA-OR-A5J2-01","TCGA-OR-A5J6-01"),
data_type = data_type), "*")
# HERE
# study_id = incorrect, profile = correct ~ Throw message ignoring study_id
expect_message(.get_data_by_sample(
study_id = "not_here",
molecular_profile_id = "acc_tcga_mutations",
sample_id = c("TCGA-OR-A5J2-01","TCGA-OR-A5J6-01"),
data_type = data_type), "You have passed*")
# study_id = NULL, profile = correct - WORKS - guesses study ID
expect_error(.get_data_by_sample(
study_id = NULL,
molecular_profile_id = "acc_tcga_mutations",
sample_id = c("TCGA-OR-A5J2-01","TCGA-OR-A5J6-01"),
data_type = data_type), NA)
# study_id = correct, profile = incorrect -FAIL Informative Error
expect_error(.get_data_by_sample(
study_id = "acc_tcga",
molecular_profile_id = "nope",
sample_id = c("TCGA-OR-A5J2-01","TCGA-OR-A5J6-01"),
data_type = data_type), "Molecular*")
#study_id = incorrect, profiles = incorrect - gives informative error
expect_error(.get_data_by_sample(
study_id = "blah",
molecular_profile_id = "wrong",
sample_id = c("TCGA-OR-A5J2-01","TCGA-OR-A5J6-01"),
data_type = data_type), "Molecular profile*")
# study ID = correct, profile = NULL - gives informative error
expect_error(.get_data_by_sample(
study_id = NULL,
molecular_profile_id = "blah",
sample_id = c("TCGA-OR-A5J2-01","TCGA-OR-A5J6-01"),
data_type = data_type), "Molecular*")
# study ID = correct, profile = NULL -WORKS- looks up profile ID
expect_error(.get_data_by_sample(
study_id = "acc_tcga",
molecular_profile_id = NULL,
sample_id = c("TCGA-OR-A5J2-01","TCGA-OR-A5J6-01"),
data_type = data_type), NA)
# study_id = incorrect, profile = NULL **API fail error (could be more informative)
expect_error(.get_data_by_sample(
study_id = "not_here",
molecular_profile_id = NULL,
sample_id = c("TCGA-OR-A5J2-01","TCGA-OR-A5J6-01"),
data_type = data_type), "API*")
# study_id = NULL, profile = NULL ~ uses default study
expect_error(.get_data_by_sample(
study_id = NULL,
molecular_profile_id = NULL,
sample_id = c("TCGA-OR-A5J2-01","TCGA-OR-A5J6-01"),
data_type = data_type), NA)
# Other-------------
# no sample IDs passed
expect_error(.get_data_by_sample(
study_id = "acc_tcga",
molecular_profile_id = NULL,
data_type = data_type), "You must pass*")
# study_id > 1 passed
expect_error(.get_data_by_sample(
study_id = c("acc_tcga", "tt"),
sample_id = c("TCGA-OR-A5J2-01","TCGA-OR-A5J6-01"),
molecular_profile_id = NULL,
data_type = data_type), "More*")
# both correct, but bad base URL
expect_error(.get_data_by_sample(study_id = "acc_tcga",
molecular_profile_id = "acc_tcga_mutations",
sample_id = c("TCGA-OR-A5J2-01","TCGA-OR-A5J6-01"),
data_type = data_type, base_url = "plunk"), "API*")
# both exist but mismatched- ignores study ID but works
expect_error(.get_data_by_sample(study_id = "acc_tcga",
molecular_profile_id = "mpnst_mskcc_mutations",
sample_id = c("TCGA-OR-A5J2-01","TCGA-OR-A5J6-01"),
data_type = data_type), NA)
# fusions don't exist
expect_error(.get_data_by_sample(
study_id = "acc_tcga",
sample_id = c("TCGA-OR-A5J2-01","TCGA-OR-A5J6-01"),
molecular_profile_id = "acc_tcga_structural_variants", data_type = "fusion"), "Molecular profile*")
})
test_that("Test sample-study pairs df", {
skip_on_cran()
skip_if(httr::http_error("www.cbioportal.org/api"))
db_test <- "public"
set_cbioportal_db(db = db_test)
data_type = "mutation"
# works ---
df_pairs <- data.frame(
"sample_id" = c("P-0002146-T01-IM3", "s_C_CAUWT7_P001_d"),
"study_id" = c("blca_plasmacytoid_mskcc_2016", "prad_msk_2019"))
expect_error(.get_data_by_sample(sample_study_pairs = df_pairs,
data_type = data_type), NA)
# doesn't work (for now) ---
df_pairs <- data.frame(
"sample_id" = c("P-0002146-T01-IM3", "s_C_CAUWT7_P001_d"),
"molecular_profile_id" = c("blca_plasmacytoid_mskcc_2016_mutations", "prad_msk_2019_mutations"))
expect_error(.get_data_by_sample(sample_study_pairs = df_pairs,
data_type = "fusion"), "*")
# need colnames ---
df_pairs <- data.frame(
"wrong" = c("P-0002146-T01-IM3", "s_C_CAUWT7_P001_d"),
"study_id" = c("blca_plasmacytoid_mskcc_2016", "prad_msk_2019"))
expect_error(.get_data_by_sample(sample_study_pairs = df_pairs,
data_type = data_type), "*")
# need colnames ---
df_pairs <- data.frame(
"sample_id" = c("P-0002146-T01-IM3", "s_C_CAUWT7_P001_d"),
"wrong" = c("blca_plasmacytoid_mskcc_2016", "prad_msk_2019"))
expect_error(.get_data_by_sample(sample_study_pairs = df_pairs,
data_type = data_type), "*")
# approximate colnames work ---
sample_study_pairs <- data.frame(
"SAMPLE ID" = c("P-0002146-T01-IM3", "s_C_CAUWT7_P001_d"),
"studyID" = c("blca_plasmacytoid_mskcc_2016", "prad_msk_2019"),
"moLEcularProfile ID" = c("blca_plasmacytoid_mskcc_2016_mutations", "prad_msk_2019_mutations"))
expect_error(.get_data_by_sample(sample_study_pairs = sample_study_pairs,
data_type = data_type), NA)
#additional columns ignored ---
sample_study_pairs <- data.frame(
"SAMPLE ID" = c("P-0002146-T01-IM3", "s_C_CAUWT7_P001_d"),
"studyID" = c("blca_plasmacytoid_mskcc_2016", "prad_msk_2019"),
"moLEcularProfile ID" = c("blca_plasmacytoid_mskcc_2016_mutations", "prad_msk_2019_mutations"),
"rando" = c("h", "i"))
expect_error(.get_data_by_sample(sample_study_pairs = sample_study_pairs,
data_type = data_type), NA)
})
test_that("data is same regardless of function", {
skip_on_cran()
skip_if(httr::http_error("www.cbioportal.org/api"))
db_test <- "public"
set_cbioportal_db(db = db_test)
sample_id = c("s_C_03LNU8_P001_d", "s_C_36924L_P001_d", "s_C_CAUWT7_P001_d")
# molecular_profile_id = "mpnst_mskcc_mutations"
study_id = "prad_msk_2019"
get_gen <- get_genetics_by_sample(sample_id = sample_id,
study_id = study_id)
# Mutation
molecular_profile_id = "prad_msk_2019_mutations"
by_study <- get_mutations_by_sample(sample_id = sample_id, study_id = study_id)
by_prof <- get_mutations_by_sample(sample_id = sample_id, molecular_profile_id = molecular_profile_id)
expect_identical(by_study, by_prof, get_gen$mutation)
# CNA ---
molecular_profile_id = "prad_msk_2019_cna"
by_study <- get_cna_by_sample(sample_id = sample_id, study_id = study_id)
by_prof <- get_cna_by_sample(sample_id = sample_id, molecular_profile_id = molecular_profile_id)
expect_identical(by_study, by_prof, get_gen$cna)
# Fusions ---
molecular_profile_id = "prad_msk_2019_structural_variants"
by_study <- get_fusions_by_sample(sample_id = sample_id, study_id = study_id)
by_study2 <- get_structural_variants_by_sample(sample_id = sample_id, study_id = study_id)
by_prof <- get_fusions_by_sample(sample_id = sample_id, molecular_profile_id = molecular_profile_id)
by_prof2 <- get_structural_variants_by_sample(sample_id = sample_id, molecular_profile_id = molecular_profile_id)
expect_identical(by_study, by_study2, by_prof, by_prof2, get_gen$structural_variant)
})
test_that("Unknown Hugo Symbol returns Unk ", {
skip_on_cran()
skip_if(httr::http_error("www.cbioportal.org/api"))
set_cbioportal_db("public")
df <- get_cna_by_sample(sample_id =c("TCGA-OR-A5J2-01","TCGA-OR-A5J6-01"),
study_id = "acc_tcga")
df[16, ] <- df[15,]
df[16, 'entrezGeneId'] <- 1000000
df <- df %>% select(-"hugoGeneSymbol")
df2 <- .lookup_hugo(df)
expect_true(any(stringr::str_detect(df2$hugoGeneSymbol, "unk")))
})
test_that("Hugo Symbol is added by default", {
skip_on_cran()
skip_if(httr::http_error("www.cbioportal.org/api"))
set_cbioportal_db("public")
df <- get_genetics_by_sample(sample_id =c("TCGA-OR-A5J2-01","TCGA-OR-A5J6-01"),
study_id = "acc_tcga")
expect_true(length(df$mutation$hugoGeneSymbol) > 1)
expect_true(length(df$cna$hugoGeneSymbol) > 1)
})
test_that("`add_hugo` = FALSE doesn't add column if it's not there", {
skip_on_cran()
skip_if(httr::http_error("www.cbioportal.org/api"))
set_cbioportal_db("public")
df_hugo_false <- get_genetics_by_sample(sample_id =c("s_C_CAUWT7_P001_d",
"s_C_DU6ECC_P002_d",
"s_C_M8X42T_P002_d",
"s_C_36924L_P001_d"),
study_id = "prad_msk_2019", add_hugo = FALSE)
df_hugo_true <- get_genetics_by_sample(sample_id =c("s_C_CAUWT7_P001_d",
"s_C_DU6ECC_P002_d",
"s_C_M8X42T_P002_d",
"s_C_36924L_P001_d"),
study_id = "prad_msk_2019", add_hugo = TRUE)
expect_true(setdiff(names(df_hugo_true$mutation), names(df_hugo_false$mutation)) == "hugoGeneSymbol")
expect_true(setdiff(names(df_hugo_true$cna), names(df_hugo_false$cna)) == "hugoGeneSymbol")
expect_true(length(setdiff(names(df_hugo_true$structural_variant), names(df_hugo_false$structural_variant))) == 0)
})
test_that("`add_hugo= TRUE` warns if column already exists", {
skip_on_cran()
skip_if(httr::http_error("www.cbioportal.org/api"))
set_cbioportal_db("public")
df <- get_genetics_by_sample(sample_id =c("TCGA-OR-A5J2-01","TCGA-OR-A5J6-01"),
study_id = "acc_tcga")
expect_warning(.lookup_hugo(df$mutation), "*")
})
test_that("Returns same results as pulling by study ID ", {
skip_on_cran()
skip_if(httr::http_error("www.cbioportal.org/api"))
set_cbioportal_db("public")
all <- available_samples("blca_plasmacytoid_mskcc_2016")
resolved_genes <- cbioportalR::impact_gene_info$entrez_id %>% unlist()
x <- .get_data_by_sample(sample_id = all$sampleId,
study_id = "blca_plasmacytoid_mskcc_2016", data_type = "cna")
y <-.get_data_by_sample(sample_id = all$sampleId,
study_id = "blca_plasmacytoid_mskcc_2016", data_type = "cna")
resolved_genes <- cbioportalR::impact_gene_info$entrez_id %>% unlist()
z <-.get_data_by_sample(sample_id = all$sampleId,
study_id = "blca_plasmacytoid_mskcc_2016", data_type = "cna",
genes = resolved_genes)
expect_true(length(setdiff(x$hugoGeneSymbol, z$hugoGeneSymbol)) != 0)
})
test_that("test entrez ID to hugo symbol in get_xx_by_sample functions", {
skip_on_cran()
skip_if(httr::http_error("www.cbioportal.org/api"))
set_cbioportal_db("public")
# get all genes returned for this study
all_genes <- get_genetics_by_study(study_id = "blca_plasmacytoid_mskcc_2016")
# try to pull genetics by sample using entrez IDs
# get study ID-sample ID pairs
s1 <- available_samples("blca_plasmacytoid_mskcc_2016") %>%
transmute(sample_id = sampleId, study_id = studyId)
all_genomic_entrez <- get_genetics_by_sample(sample_study_pairs = s1,
genes = all_genes$mutation$entrezGeneId)
# convert relevant entrez IDs to hugo symbols
entrez_to_hugo <- get_hugo_symbol(all_genes$mutation$entrezGeneId)
# try to pull genetics by sample using the converted Hugo symbols
all_genomic_hugo <- get_genetics_by_sample(sample_study_pairs = s1,
genes = entrez_to_hugo$hugoGeneSymbol)
expect_equal(all_genomic_entrez$mutation, all_genomic_hugo$mutation)
expect_equal(all_genomic_entrez$cna, all_genomic_hugo$cna)
expect_equal(all_genomic_entrez$structural_variant, all_genomic_hugo$structural_variant)
})
test_that("pulling with gene ID (entrez or hugo) works with no error", {
skip_on_cran()
skip_if(httr::http_error("www.cbioportal.org/api"))
set_cbioportal_db("public")
genes = get_entrez_id(c("ERBB2", "PIK3C2G",
"CDKN1A", "EPHA2", "NOTCH2"))
s1 <- available_samples("blca_plasmacytoid_mskcc_2016") %>%
transmute(sample_id = sampleId, study_id = studyId)
gen_by_entrez <- get_genetics_by_sample(sample_study_pairs = s1,
genes = genes$entrezGeneId)
gen_by_hugo <- get_genetics_by_sample(sample_study_pairs = s1,
genes = genes$hugoGeneSymbol)
expect_true(identical(gen_by_entrez$mutation, gen_by_hugo$mutation))
expect_true(identical(gen_by_entrez$cna, gen_by_hugo$cna))
expect_true(identical(gen_by_entrez$structural_variant, gen_by_hugo$structural_variant))
})
test_that("pulling with panel ID works with no error and matches pull by gene", {
skip_on_cran()
skip_if(httr::http_error("www.cbioportal.org/api"))
set_cbioportal_db("public")
s1 <- available_samples("blca_plasmacytoid_mskcc_2016") %>%
transmute(sample_id = sampleId, study_id = studyId)
expect_error(gen_by_panel <- get_genetics_by_sample(sample_study_pairs = s1,
panel = "IMPACT468"), NA)
genes <- get_gene_panel("IMPACT468")
gen_by_entrez <- get_genetics_by_sample(sample_study_pairs = s1,
genes = genes$entrezGeneId)
expect_true(identical(gen_by_panel$mutation, gen_by_entrez$mutation))
expect_true(identical(gen_by_panel$cna, gen_by_entrez$cna))
expect_true(identical(gen_by_panel$structural_variant, gen_by_entrez$structural_variant))
})
test_that("pulling with panel ID works with no error and matches pull by gene", {
skip_on_cran()
skip_if(httr::http_error("www.cbioportal.org/api"))
set_cbioportal_db("public")
s1 <- available_samples("blca_plasmacytoid_mskcc_2016") %>%
dplyr::transmute(sample_id = sampleId, study_id = studyId)
# error if misspecified panel
expect_error(get_mutations_by_sample(sample_study_pairs = s1,
panel = "ttt"), "*")
# no error if correct panel
expect_error(gen_by_panel <- get_genetics_by_sample(sample_study_pairs = s1,
panel = "IMPACT468"), NA)
genes <- get_gene_panel("IMPACT468")
gen_by_entrez <- get_genetics_by_sample(sample_study_pairs = s1,
genes = genes$entrezGeneId)
expect_true(identical(gen_by_panel$mutation, gen_by_entrez$mutation))
expect_true(identical(gen_by_panel$cna, gen_by_entrez$cna))
expect_true(identical(gen_by_panel$structural_variant, gen_by_entrez$structural_variant))
})
test_that("pull by panel ID + gene IDs", {
skip_on_cran()
skip_if(httr::http_error("www.cbioportal.org/api"))
set_cbioportal_db("public")
s1 <- available_samples("blca_plasmacytoid_mskcc_2016") %>%
dplyr::transmute(sample_id = sampleId, study_id = studyId)
plus_gene <- "NOTCH4"
plus_entrez = get_entrez_id(plus_gene)$entrezGeneId
expect_error(gen_by_panel <- get_genetics_by_sample(sample_study_pairs = s1,
panel = "sarc_mskcc_panel", genes = plus_gene), NA)
expect_error(gen_by_panel2 <- get_genetics_by_sample(sample_study_pairs = s1,
panel = "sarc_mskcc_panel", genes = plus_entrez), NA)
expect_error(gen_by_panel3 <- get_genetics_by_sample(sample_study_pairs = s1,
panel = "sarc_mskcc_panel"), NA)
expect_true(identical(gen_by_panel$mutation, gen_by_panel2$mutation))
expect_true(identical(gen_by_panel$cna, gen_by_panel2$cna))
expect_true(identical(gen_by_panel$structural_variant, gen_by_panel2$structural_variant))
expect_equal(setdiff(gen_by_panel$mutation$hugoGeneSymbol,
gen_by_panel3$mutation$hugoGeneSymbol), plus_gene)
})
test_that("pull by two panel IDs", {
skip_on_cran()
skip_if(httr::http_error("www.cbioportal.org/api"))
set_cbioportal_db("public")
s1 <- c("DS-sig-010-P2", "DS-sig-010-P1", "DS-sig-018-P")
panels <- c("IMPACT468", "sarc_mskcc_panel")
ids <- get_gene_panel(panels) %>%
dplyr::pull(entrezGeneId) %>%
unique()
expect_error(gen_by_panel <- get_mutations_by_sample(sample_id = s1,
study_id = "blca_plasmacytoid_mskcc_2016",
panel = c("IMPACT468", "sarc_mskcc_panel"),
genes = "NOTCH2"), NA)
expect_error(gen_by_panel2 <- get_mutations_by_sample(sample_id = s1,
study_id = "blca_plasmacytoid_mskcc_2016",
panel = c("sarc_mskcc_panel"),
genes = "NOTCH2"), NA)
expect_true(length(gen_by_panel$hugoGeneSymbol) > length(gen_by_panel2$hugoGeneSymbol))
})
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