tests/testthat/test_data.R

In lcolladotor/derfinder: Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach

windowsFlag <- .Platform$OS.type != "windows"

# Setup
datadir <- system.file("extdata", "genomeData", package = "derfinder")
files <- rawFiles(
    datadir = datadir, samplepatt = "*accepted_hits.bam$",
    fileterm = NULL
)
## Shorten the column names
names(files) <- gsub("_accepted_hits.bam", "", names(files))

## Find files
bogus <- rawFiles(datadir = datadir, samplepatt = "bw")
test_that("Finding files", {
    expect_that(
        rawFiles(datadir = NULL, sampledirs = NULL),
        throws_error("Either 'samplepatt' or 'sampledirs' must be non-NULL.")
    )
    expect_that(length(bogus), equals(0))
})

## Load BAM data
dataFilt <- loadCoverage(files = files, chr = "21", cutoff = 0)
dataRaw <- loadCoverage(files = files, chr = "21", cutoff = NULL)
dataFilt.mean <- loadCoverage(
    files = files, chr = "21", cutoff = 0,
    returnMean = TRUE
)
which <- GRanges("21", IRanges(47410303, 47418067))

test_that("Load BAM data", {
    expect_that(dataFilt, is_identical_to(genomeData))
    expect_that(dataRaw, is_identical_to(genomeDataRaw))
    expect_that(names(dataFilt.mean), is_identical_to(c(
        "coverage", "position",
        "meanCoverage"
    )))
    expect_that(sum(dataFilt.mean$meanCoverage), equals(357.838709677))
    expect_that(loadCoverage(files = files[1:2], chr = "21", cutoff = 0), is_identical_to(loadCoverage(files = files[1:2], chr = "21", cutoff = 0, which = which)))
})

## Other seqnames
f1 <- system.file("extdata", "ex1.bam", package = "Rsamtools", mustWork = TRUE)
test_that("Non-standard seqnames", {
    expect_that(lapply(fullCoverage(f1, chrs = c("seq1", "seq2"), verbose = FALSE), nrow), equals(list("seq1" = 1575, "seq2" = 1584)))
    expect_that(lapply(fullCoverage(f1, chrs = c("seq1", "seq2"), verbose = FALSE), function(x) {
        sum(x[[1]])
    }), equals(list("seq1" = 52166, "seq2" = 63017)))
})

## Total mapped
test_that("Total mapped: BAM", {
    expect_equal(getTotalMapped(f1), 3271)
    expect_equal(getTotalMapped(f1), getTotalMapped(f1, "seq1") + getTotalMapped(f1, "seq2"))
})

## Export BigWig
if (windowsFlag) {
    dir.create("bw")

    test_that("Create BigWig files", {
        expect_that(
            bws <- createBw(list("chr21" = dataRaw), path = "bw"),
            gives_warning()
        )
        expect_that(is(bws, "GRangesList"), is_identical_to(TRUE))
        expect_that(length(bws), equals(31))
        expect_that(length(bws[[1]]), equals(16))
        expect_that(names(mcols(bws[[1]])), is_identical_to("score"))
        expect_that(dir("bw"), is_identical_to(c("ERR009101.bw", "ERR009102.bw", "ERR009105.bw", "ERR009107.bw", "ERR009108.bw", "ERR009112.bw", "ERR009115.bw", "ERR009116.bw", "ERR009131.bw", "ERR009138.bw", "ERR009144.bw", "ERR009145.bw", "ERR009148.bw", "ERR009151.bw", "ERR009152.bw", "ERR009153.bw", "ERR009159.bw", "ERR009161.bw", "ERR009163.bw", "ERR009164.bw", "ERR009167.bw", "SRR031812.bw", "SRR031835.bw", "SRR031904.bw")))
    })

    ## Identify BigWig files
    bigwigs <- rawFiles(datadir = "bw", samplepatt = "bw", fileterm = NULL)
    names(bigwigs) <- gsub(".bw", "", names(bigwigs))

    ## Load BigWig
    dataBW <- loadCoverage(bigwigs,
        chr = "chr21", cutoff = NULL,
        inputType = "BigWig"
    )
    dataRaw.bw <- dataRaw
    dataRaw.bw$coverage <- dataRaw.bw$coverage[, names(bigwigs)]

    test_that("Load BigWig data", {
        expect_that(dataRaw.bw, equals(dataBW))
        expect_that(loadCoverage(bigwigs,
            chr = "21", cutoff = NULL,
            inputType = "BigWig", verbose = FALSE
        ), throws_error())
        expect_that(loadCoverage(bigwigs,
            chr = "chr21", cutoff = NULL,
            verbose = FALSE
        ), equals(dataRaw.bw))
    })

    b1 <- system.file("extdata", "AMY", "HSB113.bw", package = "derfinderData")
    b2 <- BigWigFile(b1)
    test_that("AUC: BigWig", {
        expect_equal(getTotalMapped(b1), 926227.628686)
    })
}


## Loading with GenomicFiles
dataRaw.GF <- loadCoverage(files, chr = "21", tilewidth = 2e7, cutoff = NULL)
test_that("Load using GenomicFiles via BAM", {
    expect_that(dataRaw, is_identical_to(dataRaw.GF))
})
if (windowsFlag) {
    dataRaw.bw.GF <- loadCoverage(bigwigs,
        chr = "chr21", tilewidth = 2e7,
        cutoff = NULL, inputType = "BigWig"
    )
    test_that("Load using GenomicFiles via BigWig", {
        expect_that(dataBW, is_identical_to(dataRaw.bw.GF))
    })
}


## Loading with fullCoverage
fullCov <- fullCoverage(files = files, chrs = "21")
test_that("Load with fullCoverage()", {
    expect_that(list("chr21" = dataRaw$coverage), is_identical_to(fullCov))
    expect_that(fullCoverage(files = files, chrs = "21", output = c(
        "one",
        "two"
    )), throws_error())
    expect_that(fullCoverage(files = files, chrs = "21", chrlens = c(
        4e7,
        5e7
    )), throws_error())
})

if (windowsFlag) {
    fullCov.bw <- fullCoverage(
        files = bigwigs, chrs = "chr21",
        inputType = "BigWig"
    )
    test_that("Load with fullCoverage() via BigWigs", {
        expect_that(list("chr21" = dataBW$coverage), is_identical_to(fullCov.bw))
    })
}

## Loading with BamFile, BamFileList
bam <- system.file("extdata", "genomeData", "ERR009101_accepted_hits.bam", package = "derfinder")
names(bam) <- "sample1"
library("Rsamtools")
bFile <- BamFile(bam, index = paste0(bam, ".bai"))

test_that("BamFile", {
    expect_that(fullCoverage(bam, chrs = "21", verbose = FALSE), is_identical_to(fullCoverage(bFile, chrs = "21", sampleNames = "sample1", verbose = FALSE)))
    expect_that(fullCoverage(bam, chrs = "21", verbose = FALSE), is_identical_to(fullCoverage(BamFileList(bFile), chrs = "21", sampleNames = "sample1", verbose = FALSE)))
})

## Loading via BigWigFile
if (windowsFlag) {
    library("rtracklayer")
    big1 <- BigWigFile(bigwigs[1])
    big1.list <- BigWigFileList(bigwigs[1])

    test_that("BigWigFile", {
        expect_that(fullCoverage(bam, chrs = "21", sampleNames = "ERR009101", verbose = FALSE), equals(fullCoverage(big1.list, chrs = "chr21", verbose = FALSE)))
        expect_that(fullCoverage(big1.list, chrs = "chr21", verbose = FALSE), is_identical_to(fullCoverage(big1, chrs = "chr21", verbose = FALSE)))
    })
}

## Dropping D (deletions from reference) bases
test_that("CIGAR", {
    expect_that(loadCoverage(files["ERR009167"], chr = "21", drop.D = TRUE, verbose = FALSE)$coverage[[1]] - loadCoverage(files["ERR009167"], chr = "21", drop.D = FALSE, verbose = FALSE)$coverage[[1]], is_identical_to(Rle(c(0L, -1L, 0L), c(47411967, 1, 717927))))
})

## Filtering
filt <- filterData(dataRaw$coverage, cutoff = 0)
test_that("Filtering", {
    expect_that(filterData(dataRaw$coverage,
        cutoff = -1,
        verbose = FALSE
    )$coverage, is_identical_to(dataRaw$coverage))
    expect_that(filterData(dataRaw), throws_error())
    expect_that(filterData(dataRaw$coverage, filter = "two"), throws_error())
    expect_that(filterData(dataRaw$coverage,
        cutoff = 10,
        verbose = FALSE
    )$position, is_identical_to(Rle(FALSE, 48129895)))
    expect_that(dim(filterData(dataRaw$coverage,
        cutoff = 0.5, filter = "mean",
        verbose = FALSE
    )$coverage), equals(c(273, 31)))
    expect_that(nrow(filt$coverage), is_identical_to(sum(filt$position)))
})


## Test getRegionCoverage() and coverageToExon()

## Assign chr lengths using hg19 information, use only first two regions
library("GenomicRanges")

chr.lens <- c(249250621, 243199373, 198022430, 191154276, 180915260, 171115067, 159138663, 146364022, 141213431, 135534747, 135006516, 133851895, 115169878, 107349540, 102531392, 90354753, 81195210, 78077248, 59128983, 63025520, 48129895, 51304566, 155270560, 59373566)
names(chr.lens) <- paste0("chr", c(1:22, "X", "Y"))


regions <- genomeRegions$regions[1:2]
seqlengths(regions) <- seqlengths(getChromInfoFromUCSC("hg19",
    as.Seqinfo = TRUE
))[
    mapSeqlevels(names(seqlengths(regions)), "UCSC")
]

test_that("Chr lengths", {
    expect_equal(seqlengths(regions), chr.lens["chr21"])
})

## Get the region coverage
regionCov <- getRegionCoverage(fullCov = fullCov, regions = regions)

## Load using which
fullCov.regs <- fullCoverage(files, chrs = seqlevels(regions), fileStyle = "NCBI", protectWhich = 3e4, which = regions, verbose = FALSE)

## Load without using the default 'protectWhich'
max.noP <- sapply(loadCoverage(files = files, chr = "21", verbose = FALSE, protectWhich = 0, cutoff = NULL, which = regions, fileStyle = "NCBI")$coverage, max)
max.wP <- sapply(fullCov$chr21, max)

## Use only the first two exons
smallGenomicState <- genomicState
smallGenomicState$fullGenome <- smallGenomicState$fullGenome[which(smallGenomicState$fullGenome$theRegion == "exon")[1:2]]

## Get the coverage information for each exon
exonCov <- coverageToExon(
    fullCov = fullCov,
    genomicState = smallGenomicState$fullGenome, L = 36
)

## Verify coverageToExon
exonCov.verify <- do.call(rbind, lapply(getRegionCoverage(regions = smallGenomicState$fullGenome, files = files, fileStyle = "NCBI", verbose = FALSE), function(x) {
    sapply(x, sum)
})) / 36

## Test call using multiple cores for coverageToExon()
tmp <- rep(smallGenomicState$fullGenome, 3)
seqlevels(tmp) <- c("chr20", "chr21", "chr22")
seqnames(tmp) <- rep(c("chr20", "chr21", "chr22"), 2)
names(tmp) <- 1:6
strand(tmp) <- rep(c("+", "-"), 3)
tripleSmall <- smallGenomicState
tripleSmall$fullGenome <- tmp

test_that("Obtaining region coverage", {
    expect_that(fullCov, is_identical_to(fullCov.regs))
    expect_that(regionCov, is_identical_to(getRegionCoverage(regions = regions, files = files, fileStyle = "NCBI", verbose = FALSE)))
    expect_that(exonCov, is_identical_to(coverageToExon(genomicState = smallGenomicState$fullGenome, L = 36, files = files, fileStyle = "NCBI", verbose = FALSE)))
    expect_that(max.noP - max.wP, is_equivalent_to(rep(c(0, -1, 0, -1, -2, -1, -3, 0, -3, -1, -3, 0, -1, 0, -1, 0), c(4, 1, 1, 1, 3, 2, 2, 1, 3, 1, 2, 1, 1, 3, 1, 4))))
    expect_that(exonCov, equals(exonCov.verify))
    expect_that(coverageToExon(fullCov = fullCov, genomicState = tripleSmall$fullGenome, L = 36, strandCores = 1, mc.cores = 10), equals(coverageToExon(fullCov = fullCov, genomicState = tripleSmall$fullGenome, L = 36, BPPARAM.strandStep = BiocParallel::SerialParam(), mc.cores = 10)))
})

## Naming
x <- Rle(round(runif(1e4, max = 10)))
y <- Rle(round(runif(1e4, max = 10)))
z <- Rle(round(runif(1e4, max = 10)))
l <- list("(CEU)" = x, "(YRI)" = y, "[0,-5)" = z)
filt <- filterData(l, 5)
test_that("Naming is preserved", {
    expect_equal(colnames(filt$coverage), names(l))
})


## Clean up
if (windowsFlag) {
    unlink("bw", recursive = TRUE)
}