context("Download and prepare")
test_that("GDCdownload API method is working ", {
skip_on_bioc()
skip_if_offline()
cases <- c(
"TCGA-PA-A5YG-01A-11R-A29S-07",
"TCGA-OR-A5JX-01A-11R-A29S-07",
"TCGA-PK-A5HA-01A-11R-A29S-07",
"TCGA-OR-A5KY-01A-11R-A29S-07"
)
acc <- GDCquery(
project = c("TCGA-ACC"),
data.category = "Transcriptome Profiling",
data.type = "Gene Expression Quantification",
workflow.type = "STAR - Counts",
barcode = substr(cases,1,12)
)
GDCdownload(acc, method = "api", directory = "ex")
obj <- GDCprepare(acc, directory = "ex",summarizedExperiment = TRUE)
expect_true(all(substr(colnames(obj),1,12) == substr(cases,1,12)))
expect_true(all(obj$barcode == cases))
# Checking the data matches the file for a random gene
expect_equal(assays(obj)$unstranded["ENSG00000003756.17","TCGA-PK-A5HA-01A-11R-A29S-07"], 3584)
expect_equal(assays(obj)$stranded_first["ENSG00000003756.17","TCGA-PK-A5HA-01A-11R-A29S-07"], 2628)
expect_equal(assays(obj)$stranded_second["ENSG00000003756.17","TCGA-PK-A5HA-01A-11R-A29S-07"], 2612)
expect_equal(assays(obj)$tpm_unstrand["ENSG00000003756.17","TCGA-PK-A5HA-01A-11R-A29S-07"], 13.2758)
expect_equal(assays(obj)$fpkm_unstrand["ENSG00000003756.17","TCGA-PK-A5HA-01A-11R-A29S-07"], 7.0563)
expect_equal(assays(obj)$fpkm_uq_unstrand["ENSG00000003756.17","TCGA-PK-A5HA-01A-11R-A29S-07"], 9.8086)
query <- GDCquery(
project = "CPTAC-3",
data.category = "Transcriptome Profiling",
data.type = "Gene Expression Quantification",
workflow.type = "STAR - Counts",
barcode = c("CPT0010260013","CPT0000870008","CPT0105190006","CPT0077490006")
)
GDCdownload(query)
data <- GDCprepare(query)
expect_true(all(query$results[[1]]$sample.submitter_id == colnames(data)))
expect_true(all(query$results[[1]]$sample.submitter_id == data$sample_submitter_id))
})
test_that("getBarcodeInfo works", {
skip_on_bioc()
skip_if_offline()
cols <- c("gender","project_id","days_to_last_follow_up","alcohol_history")
x <- getBarcodeInfo(c("TCGA-OR-A5LR-01A", "TCGA-OR-A5LJ-01A"))
expect_true(all(cols %in% colnames(x)))
cols <- c("gender","project_id")
x <- getBarcodeInfo(c("TARGET-20-PARUDL-03A"))
expect_true(all(cols %in% colnames(x)))
samples <- c(
"HCM-CSHL-0063-C18-85A",
"HCM-CSHL-0065-C20-06A",
"HCM-CSHL-0065-C20-85A",
"HCM-CSHL-0063-C18-01A"
)
x <- colDataPrepare(samples)
expect_true(all(rownames(x) == samples))
expect_true(x[x$sample_submitter_id == "HCM-CSHL-0065-C20-06A","gender"] == "male")
expect_true(x[x$sample_submitter_id == "HCM-CSHL-0065-C20-06A","tumor_grade"] == "G2")
expect_true(x[x$sample_submitter_id == "HCM-CSHL-0065-C20-06A","ajcc_pathologic_stage"] == "Stage IVA")
expect_true(x[x$sample_submitter_id == "HCM-CSHL-0065-C20-06A","sample_type"] == "Metastatic")
expect_true(x[x$sample_submitter_id == "HCM-CSHL-0063-C18-85A","sample_type"] == "Next Generation Cancer Model")
x <- getBarcodeInfo(
c("HCM-CSHL-0063-C18-85A",
"HCM-CSHL-0065-C20-06A",
"HCM-CSHL-0065-C20-85A",
"TARGET-20-PARUDL-03A",
"TCGA-OR-A5LR-01A",
"HCM-CSHL-0063-C18-01A")
)
expect_true(x[x$sample_submitter_id == "HCM-CSHL-0065-C20-06A","gender"] == "male")
expect_true(x[x$sample_submitter_id == "HCM-CSHL-0065-C20-06A","tumor_grade"] == "G2")
expect_true(x[x$sample_submitter_id == "HCM-CSHL-0065-C20-06A","ajcc_pathologic_stage"] == "Stage IVA")
expect_true(x[x$sample_submitter_id == "HCM-CSHL-0065-C20-06A","sample_type"] == "Metastatic")
expect_true(x[x$sample_submitter_id == "HCM-CSHL-0063-C18-85A","sample_type"] == "Next Generation Cancer Model")
})
test_that("colDataPrepare handle replicates", {
skip_on_bioc()
skip_if_offline()
barcodes <- c("TCGA-06-0156-01A-02R-1849-01","TCGA-06-0156-01A-03R-1849-01")
x <- colDataPrepare(barcodes)
expect_true(nrow(x) == 2)
expect_true(all(rownames(x) == c("TCGA-06-0156-01A-02R-1849-01","TCGA-06-0156-01A-03R-1849-01")))
expect_true(all(x$barcode == c("TCGA-06-0156-01A-02R-1849-01","TCGA-06-0156-01A-03R-1849-01")))
})
test_that("GDCprepare accepts more than one project", {
skip_on_bioc()
skip_if_offline()
cases <- c(
"TCGA-OR-A5JX-01A",
"TCGA-OR-A5J3-01A",
"TCGA-06-0680-11A",
"TCGA-14-0871-01A"
)
expect_true(all(c("TCGA-ACC","TCGA-GBM") %in% colDataPrepare(cases)$project_id))
query_acc_gbm <- GDCquery(
project = c("TCGA-ACC","TCGA-GBM"),
data.category = "Transcriptome Profiling",
data.type = "Gene Expression Quantification",
workflow.type = "STAR - Counts",
barcode = substr(cases, 1, 12)
)
GDCdownload(query_acc_gbm, method = "api", directory = "ex")
obj <- GDCprepare(query_acc_gbm, directory = "ex")
expect_true(all(c("TCGA-ACC","TCGA-GBM") %in% SummarizedExperiment::colData(obj)$project_id))
})
test_that("Non TCGA data is processed", {
skip_on_bioc()
skip_if_offline()
proj <- "MMRF-COMMPASS"
query <- GDCquery(
project = proj,
data.category = "Transcriptome Profiling",
data.type = "Gene Expression Quantification",
workflow.type = "STAR - Counts"
)
query <- GDCquery(
project = proj,
data.category = "Transcriptome Profiling",
data.type = "Gene Expression Quantification",
workflow.type = "STAR - Counts",
barcode = getResults(query)$cases[1:4]
)
})
test_that("Gene Level Copy Number is being correctly prepare", {
skip_on_bioc()
skip_if_offline()
query <- GDCquery(
project = "TCGA-ACC",
data.category = "Copy Number Variation",
data.type = "Gene Level Copy Number",
access = "open",
barcode = c("TCGA-OR-A5JD","TCGA-OR-A5J7")
)
GDCdownload(query,directory = "ex")
data <- GDCprepare(query,directory = "ex")
expect_true(all(substr(colnames(data),1,12) == c("TCGA-OR-A5JD","TCGA-OR-A5J7")))
unlink("ex", recursive = TRUE, force = TRUE)
})
test_that("DNAm files is processed correctly", {
skip_on_bioc()
skip_if_offline()
query_met.hg38 <- GDCquery(
project = "TCGA-BRCA",
data.category = "DNA Methylation",
data.type = "Methylation Beta Value",
platform = "Illumina Human Methylation 27",
barcode = c("TCGA-B6-A0IM","TCGA-A2-A0CL","TCGA-E2-A158","TCGA-AN-A0AR")
)
GDCdownload(query_met.hg38)
data.hg38 <- GDCprepare(query_met.hg38)
expect_lt(abs(assay(data.hg38)["cg16739396","TCGA-E2-A158-01A-11D-A12E-05"] - 0.0688655418909783),10^-10)
})
test_that("Prepare samples without clinical data", {
skip_on_bioc()
skip_if_offline()
# x <- GDCquery_clinic(project = "TCGA-LUAD", type = "clinical")
# x[is.na(x$diagnosis_id),]
x <- colDataPrepare(c("TCGA-80-5608-01A","TCGA-17-Z053-01A","TCGA-78-7158-01A"))
expect_true(nrow(x) == 3)
})
test_that("Prepare multiple samples from the same patient", {
skip_on_bioc()
skip_if_offline()
# https://portal.gdc.cancer.gov/cases/d7d3de82-802d-4664-8e42-d40408b129b0?bioId=548a300f-a7eb-4dc0-b9bc-5a643ef03d5d
x <- colDataPrepare(c("BA2691R","BA2577R","BA2748R","BA2577D"))
expect_true(nrow(x) == 4)
expect_equal(x["BA2748R","sample_type"],"Primary Blood Derived Cancer - Bone Marrow")
expect_equal(x["BA2577D","sample_type"],"Recurrent Blood Derived Cancer - Bone Marrow")
expect_true("age_at_diagnosis" %in% colnames(x))
})
test_that("Preparing RRPA files with number of proteins works", {
skip_on_bioc()
skip_if_offline()
query_rppa <- GDCquery(
project = c("TCGA-COAD"),
data.category = "Proteome Profiling",
experimental.strategy = "Reverse Phase Protein Array",
platform = "RPPA",
barcode = c("TCGA-CM-6165-01A","TCGA-DM-A28M-01A"),
data.type = "Protein Expression Quantification"
)
GDCdownload(query_rppa)
expect_message(
object = {
data_rppa <- GDCprepare(query_rppa)
},
regexp = "Some files have a different number of proteins, we will introduce NA for the missing values"
)
expect_true(is(data_rppa,"data.frame"))
})
