tests/testthat/test_isore.R

In bambu: Reference-guided isoform reconstruction and quantification for long read RNA-Seq data

context("Isoform reconstruction")


test_that("isore.constructReadClasses completes successfully", {
    readGrgList <- readRDS(system.file("extdata",
        "readGrgList_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds",
        package = "bambu"
    ))
    gr <- readRDS(system.file("extdata",
        "annotationGranges_txdbGrch38_91_chr9_1_1000000.rds",
        package = "bambu"
    ))
    genomeSequence <- system.file("extdata",
        "Homo_sapiens.GRCh38.dna_sm.primary_assembly_chr9_1_1000000.fa",
        package = "bambu"
    )


    seReadClassUnstrandedExpected <- readRDS(system.file("extdata",
        "seReadClassUnstranded_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds",
        package = "bambu"
    ))
    seReadClassStrandedExpected <- readRDS(system.file("extdata",
        "seReadClassStranded_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds",
        package = "bambu"
    ))

    seReadClassUnstranded <- isore.constructReadClasses(
        readGrgList = readGrgList,
        runName = "SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000_unstranded",
        annotationGrangesList = gr,
        genomeSequence = genomeSequence,
        stranded = FALSE,
        ncore = 1,
        verbose = FALSE
    )
    ## in case of testing on Mac
    names(seReadClassUnstranded@rowRanges@elementMetadata@listData$intronStarts) <- NULL
    names(seReadClassUnstranded@rowRanges@elementMetadata@listData$intronEnds) <- NULL
    expect_equal(seReadClassUnstranded, seReadClassUnstrandedExpected)


    seReadClassStranded <- isore.constructReadClasses(
        readGrgList = readGrgList,
        runName = "SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000_stranded",
        annotationGrangesList = gr,
        genomeSequence = genomeSequence,
        stranded = TRUE,
        ncore = 1,
        verbose = FALSE
    )
    names(seReadClassStranded@rowRanges@elementMetadata@listData$intronStarts) <- NULL
    names(seReadClassStranded@rowRanges@elementMetadata@listData$intronEnds) <- NULL
    expect_equal(seReadClassStranded, seReadClassStrandedExpected)
})

test_that("isore.combineTranscriptCandidates completes successfully", {
    seReadClass1 <- readRDS(system.file("extdata",
        "seReadClassUnstranded_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds",
        package = "bambu"
    ))
    seReadClass2 <- readRDS(system.file("extdata",
        "seReadClassStranded_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds",
        package = "bambu"
    ))

    seIsoReRefExpected <- readRDS(system.file("extdata",
        "seIsoReRef_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds",
        package = "bambu"
    ))
    seIsoReCombinedExpected <- readRDS(system.file("extdata",
        "seIsoReCombined_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds",
        package = "bambu"
    ))

    seIsoReRef <- isore.combineTranscriptCandidates(
        readClassSe = seReadClass1,
        readClassSeRef = NULL,
        stranded = FALSE,
        verbose = FALSE
    )
    expect_equal(seIsoReRef, seIsoReRefExpected)

    seIsoReCombined <- isore.combineTranscriptCandidates(
        readClassSe = seReadClass2,
        readClassSeRef = seIsoReRef,
        stranded = FALSE,
        verbose = FALSE
    )

    expect_equal(seIsoReCombined, seIsoReCombinedExpected)
    expect_named(assays(seIsoReCombined), c("counts", "start", "end"))
    expect_named(
        rowData(seIsoReCombined),
        c("chr", "start", "end", "strand", "intronStarts", "intronEnds", "confidenceType")
    )
})


test_that("isore.extendAnnotations completes successfully", {
    seIsoReCombined <- readRDS(system.file("extdata",
        "seIsoReCombined_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds",
        package = "bambu"
    ))
    gr <- readRDS(system.file("extdata",
        "annotationGranges_txdbGrch38_91_chr9_1_1000000.rds",
        package = "bambu"
    ))

    extendedAnnotationsExpected <- readRDS(system.file("extdata",
        "extendedAnnotationGranges_txdbGrch38_91_chr9_1_1000000.rds",
        package = "bambu"
    ))

    extendedAnnotations <- isore.extendAnnotations(
        se = seIsoReCombined,
        annotationGrangesList = gr,
        remove.subsetTx = TRUE,
        min.readCount = 2,
        min.readFractionByGene = 0.05,
        min.sampleNumber = 1,
        min.exonDistance = 35,
        min.exonOverlap = 10,
        prefix = "",
        verbose = FALSE
    )
    expect_equal(extendedAnnotations, extendedAnnotationsExpected)
})


test_that("isore.estimateDistanceToAnnotations completes successfully", {
    seReadClass1 <- readRDS(system.file("extdata",
        "seReadClassUnstranded_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds",
        package = "bambu"
    ))
    extendedAnnotations <- readRDS(system.file("extdata",
        "extendedAnnotationGranges_txdbGrch38_91_chr9_1_1000000.rds",
        package = "bambu"
    ))

    seWithDist <- isore.estimateDistanceToAnnotations(
        seReadClass = seReadClass1,
        annotationGrangesList = extendedAnnotations,
        min.exonDistance = 35
    )
    names(seWithDist@metadata$distTable$readCount) <- NULL
    expect_equal(seWithDist, seWithDistExpected)
})