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context("query_clinical")
test_that("TCGAquery_SampleTypes returns the correct barcodes", {
barcode <- c("TCGA-B0-4698-01Z-00-DX1","TCGA-CZ-4863-02Z-00-DX1")
expect_equal(TCGAquery_SampleTypes(barcode,c("TR")),barcode[2])
expect_equal(TCGAquery_SampleTypes(barcode,c("TP","TR")),barcode)
expect_equal(TCGAquery_SampleTypes(barcode,c("TP")),barcode[1])
expect_equal(TCGAquery_SampleTypes(barcode,c("TN")),"Error message: one or more sample types do not exist")
})
skip("Skip test downloading data")
test_that("GDCquery_clinic populates correctly the data", {
skip_on_bioc()
results <- GDCquery_clinic(project = "BEATAML1.0-COHORT")
results.2028 <- results[results$submitter_id == "2028",]
expect_equal(results.2028$vital_status,"Alive")
expect_true(
all(c("BA2486D","BA2144D") %in%
(str_split(results.2028$submitter_sample_ids,",") %>% unlist()))
)
expect_equal(results.2028$age_at_diagnosis %>% as.numeric() %% 365.25,134)
expect_equal(as.integer(results.2028$age_at_diagnosis %>% as.numeric() / 365.25),56)
results <- GDCquery_clinic(project = "ORGANOID-PANCREATIC", type = "clinical")
results.42 <- results[results$submitter_id == "42",]
expect_equal(results.42$ajcc_pathologic_stage,"Stage IIA")
expect_equal(results.42$ethnicity,"not hispanic or latino")
expect_equal(as.integer(results.2028$age_at_diagnosis %>% as.numeric() / 365.25),56)
results <- GDCquery_clinic(project = "TCGA-LUAD")
results.sample <- results[results$submitter_id == "TCGA-80-5608",]
expect_equal(results.sample$vital_status,"Alive")
expect_equal(results.sample$gender,"female")
expect_equal(results.sample$ajcc_pathologic_stage,"Stage IA")
# Sample without clinical data
results.sample <- results[results$submitter_id == "TCGA-17-Z031",]
expect_true(is.na(results.sample$vital_status))
expect_true(is.na(results.sample$gender))
expect_true(is.na(results.sample$ajcc_pathologic_stage))
})
test_that("TCGAquery_MatchedCoupledSampleTypes returns the correct barcodes", {
barcode <- c(
"TCGA-B0-4698-01Z-00-DX1",
"TCGA-B0-4698-02Z-00-DX1",
"TCGA-CD-4698-02Z-00-DX1",
"TCGA-XO-4698-01Z-00-DX1",
"TCGA-XO-4698-11Z-00-DX1"
)
expect_equal(TCGAquery_MatchedCoupledSampleTypes(barcode, c("TP","TR")),barcode[1:2])
expect_equal(TCGAquery_MatchedCoupledSampleTypes(barcode, c("TP","NT")),barcode[4:5])
expect_equal(TCGAquery_MatchedCoupledSampleTypes(barcode,c("TN","TP")),"Error message: one or more sample types do not exist")
expect_equal(TCGAquery_MatchedCoupledSampleTypes(barcode,c("TN")),"Error message: exactly two types need to be provided")
})
test_that("TCGAquery_subtype returns the a data frame if exists data", {
expect_equal(class(TCGAquery_subtype("lgg")),class(data.frame()))
expect_equal(class(TCGAquery_subtype("all")),class(data.frame()))
expect_error(TCGAquery_subtype("f"))
})
test_that("GDCprepare_clinic works if no follow up data is available", {
skip_on_bioc()
skip_if_offline()
query <- GDCquery(
project = "TCGA-LAML",
data.category = "Clinical",
data.format = "bcr xml"
)
GDCdownload(
query = query,
directory = "."
)
clinical <- GDCprepare_clinic(
query = query,
directory = ".",
clinical.info = "patient"
)
})
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