tests/testthat/test-query.R

In TCGAbiolinks: TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data

context("Query")


test_that("GDCquery can filter by data.category", {
    skip_on_bioc()
    skip_if_offline()

    query <- GDCquery(project = "TCGA-ACC",data.category = "Copy Number Variation")
    expect_equal(unique(query$results[[1]]$data_category),"Copy Number Variation")
    query <- GDCquery(project = "TCGA-ACC",data.category = "Copy Number Variation", data.type = "Copy Number Segment")
    expect_equal(unique(query$results[[1]]$data_type),"Copy Number Segment")
})

test_that("GDCquery accepts more than one project", {
    skip_on_bioc()
    skip_if_offline()

    acc <- GDCquery(project = "TCGA-ACC",
                    data.category = "Copy Number Variation",
                    data.type = "Copy Number Segment")
    gbm <- GDCquery(project = "TCGA-GBM",
                    data.category = "Copy Number Variation",
                    data.type = "Copy Number Segment")
    acc.gbm <- GDCquery(project =  c("TCGA-ACC","TCGA-GBM"),
                        data.category = "Copy Number Variation",
                        data.type = "Copy Number Segment")
    expect_equal(unique(acc.gbm$results[[1]]$data_type),"Copy Number Segment")
    expect_equal(nrow(acc.gbm$results[[1]]), sum(nrow(acc$results[[1]]),nrow(gbm$results[[1]])))
    expect_true(nrow(dplyr::anti_join(acc$results[[1]],acc.gbm$results[[1]], by = "file_id")) == 0)
    expect_true(nrow(dplyr::anti_join(gbm$results[[1]],acc.gbm$results[[1]], by = "file_id")) == 0)
    expect_true(nrow(dplyr::anti_join(acc.gbm$results[[1]],acc$results[[1]], by = "file_id")) == nrow(gbm$results[[1]]))
})

test_that("GDCquery can filter by sample.type", {
    skip_on_bioc()
    skip_if_offline()

    sample.type <- "Primary Tumor"
    query <- GDCquery(project = "TCGA-ACC",
                      data.category =  "Copy Number Variation",
                      data.type = "Masked Copy Number Segment",
                      sample.type = sample.type)
    expect_equal(as.character(unique(query$results[[1]]$sample_type)),sample.type)

    sample.type <- "Solid Tissue Normal"
    query <- GDCquery(project = "TCGA-ACC",
                      data.category =  "Copy Number Variation",
                      data.type = "Masked Copy Number Segment",
                      sample.type = sample.type)
    expect_equal(as.character(unique(query$results[[1]]$sample_type)),sample.type)

    sample.type <- "Solid Tissue Normal"
    query <- GDCquery(project =  c("TCGA-COAD"),
                        data.category = "Transcriptome Profiling",
                        data.type = "Gene Expression Quantification",
                        workflow.type = "HTSeq - FPKM-UQ",
                        sample.type = sample.type)
    expect_equal(as.character(unique(query$results[[1]]$sample_type)),sample.type)


    sample.type <- "Solid Tissue Normal"
    query <- GDCquery(project = "TCGA-BRCA",
                     legacy = TRUE,
                     data.category = "Gene expression",
                     data.type = "Gene expression quantification",
                     platform = "Illumina HiSeq",
                     file.type = "results",
                     experimental.strategy = "RNA-Seq",
                     sample.type = sample.type)
    expect_equal(as.character(unique(query$results[[1]]$sample_type)),sample.type)



    sample.type <- c("Solid Tissue Normal", "Primary Tumor")
    query <- GDCquery(project = "TCGA-ACC",
                      data.category =  "Copy Number Variation",
                      data.type = "Masked Copy Number Segment",
                      sample.type = sample.type)
    expect_true(all(sample.type %in% unique(query$results[[1]]$sample_type)))
})

test_that("GDCquery can filter by barcode", {
    skip_on_bioc()
    skip_if_offline()

    barcode <- c("TARGET-20-PADZCG-04A-01R","TARGET-20-PARJCR-09A-01R")
    query <- GDCquery(project = "TARGET-AML",
                      data.category = "Transcriptome Profiling",
                      data.type = "Gene Expression Quantification",
                      workflow.type = "HTSeq - Counts",
                      barcode = barcode)
    expect_true(all(sort(barcode) == sort(unique(query$results[[1]]$cases))))
    barcode <- c( "TCGA-OR-A5KU-01A-11D-A29H-01", "TCGA-OR-A5JK-01A-11D-A29H-01")
    query <- GDCquery(project = "TCGA-ACC",
                      data.category = "Copy Number Variation",
                      data.type = "Copy Number Segment",
                      barcode = barcode)
    expect_true(all(sort(barcode) == sort(unique(query$results[[1]]$cases))))
    barcode <- c("TCGA-OR-A5KU", "TCGA-OR-A5JK")
    query <- GDCquery(project = "TCGA-ACC",
                      data.category = "Clinical",
                      file.type = "xml",
                      barcode = barcode)
    expect_true(all(sort(barcode) == sort(unique(query$results[[1]]$cases))))

    # Will work if barcode was not found
    query <- GDCquery(project = "TCGA-BRCA", data.category = "Clinical",file.type = "xml",
                           barcode = c("TCGA-3C-AALK","TCGA-A2-A04Q","TCGA-A4-A04Q"))
    expect_true(!all(c("TCGA-3C-AALK","TCGA-A2-A04Q","TCGA-A4-A04Q") %in% query$results[[1]]$cases))
})

test_that("GDCquery can filter copy number from legacy data by file type. Case: nocnv_hg18", {
    skip_on_bioc()
    skip_if_offline()

    query <- GDCquery(project = "TCGA-ACC",
                      data.category =  "Copy number variation",
                      legacy = TRUE,
                      file.type = "nocnv_hg18.seg",
                      barcode = c("TCGA-OR-A5LR-01A-11D-A29H-01"))
    expect_equal(query$results[[1]]$file_name,"AQUAE_p_TCGA_112_304_b2_N_GenomeWideSNP_6_D10_1348300.nocnv_hg18.seg.txt")
})

test_that("GDCquery can filter copy number from legacy data by file type. Case: hg18", {
    skip_on_bioc()
    skip_if_offline()

    query <- GDCquery(project = "TCGA-ACC",
                      data.category =  "Copy number variation",
                      legacy = TRUE,
                      file.type = "hg18.seg",
                      barcode = c("TCGA-OR-A5LR-01A-11D-A29H-01"))
    expect_equal(query$results[[1]]$file_name,"AQUAE_p_TCGA_112_304_b2_N_GenomeWideSNP_6_D10_1348300.hg18.seg.txt")
})

test_that("GDCquery can filter copy number from legacy data by file type. Case: hg19", {
    skip_on_bioc()
    skip_if_offline()

    query <- GDCquery(project = "TCGA-ACC",
                      data.category =  "Copy number variation",
                      legacy = TRUE,
                      file.type = "hg19.seg",
                      barcode = c("TCGA-OR-A5LR-01A-11D-A29H-01"))
    expect_equal(query$results[[1]]$file_name,"AQUAE_p_TCGA_112_304_b2_N_GenomeWideSNP_6_D10_1348300.hg19.seg.txt")
})


test_that("GDCquery can filter copy number from legacy data by file type. Case: nocnv_hg19", {
    skip_on_bioc()
    skip_if_offline()

    query <- GDCquery(project = "TCGA-ACC",
                      data.category =  "Copy number variation",
                      legacy = TRUE,
                      file.type = "nocnv_hg19.seg",
                      barcode = c("TCGA-OR-A5LR-01A-11D-A29H-01"))
    expect_equal(query$results[[1]]$file_name,"AQUAE_p_TCGA_112_304_b2_N_GenomeWideSNP_6_D10_1348300.nocnv_hg19.seg.txt")

})


test_that("GDCquery can filter by access level", {
    skip_on_bioc()
    skip_if_offline()

    query <- GDCquery(project = "TCGA-KIRP",
                      data.category = "Simple Nucleotide Variation",
                      access = "open")
    expect_equal(unique(query$results[[1]]$access),"open")
    query <- GDCquery(project = "TCGA-KIRP",
                      data.category = "Simple Nucleotide Variation",
                      access = "controlled")
    expect_equal(unique(query$results[[1]]$access),"controlled")
})

test_that("GDCquery_Maf works", {
    skip_on_bioc()
    skip_if_offline()

    acc.maf <- GDCquery_Maf("ACC",pipelines = "muse")
    expect_true(nrow(acc.maf) > 0)
    acc.maf <- GDCquery_Maf("ACC", directory = "maf", pipelines = "muse")
    expect_true(nrow(acc.maf) > 0)
    unlink("GDCdata",recursive = TRUE, force = TRUE)
    unlink("maf",recursive = TRUE, force = TRUE)
})


test_that("getNbFiles and getNbCases works", {
    skip_on_bioc()
    skip_if_offline()

    aux <- getProjectSummary("TCGA-LUAD",TRUE)
    files <- getNbFiles("TCGA-LUAD","Raw microarray data",legacy = T)
    cases <- getNbCases("TCGA-LUAD","Raw microarray data")
    expect_true(cases < files)
})