tests/testthat/test-int_input.R

In csaw: ChIP-Seq Analysis with Windows

# This tests the basic internal input functions.
# library(testthat); library(csaw); source("test-int_input.R")

set.seed(320000)
test_that(".activeChrs works correctly", {
    chromos <- c(chrA=1000L, chrB=3000L)
    obam1 <- regenSE(100, chromos, outfname=tempfile())
    obam2 <- regenPE(100, chromos, outfname=tempfile())
    obam3 <- regenPE(100, c(chromos, chrC=200), outfname=tempfile())
    obam4 <- regenPE(100, chromos * 2, outfname=tempfile())

    # In the simplest case... 
    expect_identical(csaw:::.activeChrs(obam1, NULL), chromos)
    expect_identical(csaw:::.activeChrs(c(obam1, obam2), NULL), chromos)
    expect_identical(csaw:::.activeChrs(c(obam1, obam2), "chrA"), chromos["chrA"])
    expect_identical(csaw:::.activeChrs(c(obam1, obam2), "chrB"), chromos["chrB"])
    expect_identical(csaw:::.activeChrs(c(obam1, obam2), names(chromos)), chromos)

    # Triggering various warnings.
    expect_warning(out <- csaw:::.activeChrs(c(obam1, obam3), NULL), "not identical")
    expect_identical(out, chromos)
    expect_warning(out <- csaw:::.activeChrs(c(obam1, obam4), NULL), "not identical")
    expect_identical(out, chromos)
})

set.seed(320001)
test_that("automated range conversion works correctly", {
    nrows <- 200
	ncols <- 6
    counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
    rowRanges <- GRanges(rep(c("chr1", "chr2"), c(50, 150)),
                         IRanges(floor(runif(200, 1e5, 1e6)), width=100),
                         strand=sample(c("+", "-"), 200, TRUE))
    rse <- SummarizedExperiment(list(counts=counts), rowRanges=rowRanges)
    
    expect_identical(rowRanges(rse), csaw:::.toGRanges(rse))
    expect_identical(rowRanges(rse), csaw:::.toGRanges(rowRanges(rse)))
    expect_error(csaw:::.toGRanges("whee"), "must be a RangedSummarizedExperiment")
})

set.seed(320002)
test_that("test input checker is working correctly", {
    nobs <- 200L
    ids <- sample(100, nobs, replace=TRUE)
    tab <- data.frame(whee=runif(nobs), yay=seq_len(nobs))

    # Simple integer ids.
    incoming <- csaw:::.check_test_inputs(ids, tab, NULL)
    expect_identical(incoming$ids, sort(as.integer(factor(ids))))
    expect_identical(incoming$tab, tab[order(ids),])
    expect_identical(incoming$original, order(ids))
    expect_identical(incoming$weight, rep(1, nobs))
    expect_identical(incoming$groups, as.character(sort(unique(ids))))

    # Weights.
    w <- runif(nobs)
    incoming <- csaw:::.check_test_inputs(ids, tab, w)
    expect_identical(incoming$weight, w[order(ids)])

    # More complex IDs.
    ids2 <- sample(LETTERS, nobs, replace=TRUE)
    incoming <- csaw:::.check_test_inputs(ids2, tab, NULL)
    expect_identical(incoming$ids, sort(as.integer(factor(ids2))))
    expect_identical(incoming$tab, tab[order(ids2),])
    expect_identical(incoming$original, order(ids2))
    expect_identical(incoming$weight, rep(1, nobs))
    expect_identical(incoming$groups, sort(unique(ids2)))

    # Handles NAs.
    ids0 <- ids
    ids0[sample(nobs, 20)] <- NA
    out <- csaw:::.check_test_inputs(ids0, tab, NULL)
    keep <- !is.na(ids0)
    ref <- csaw:::.check_test_inputs(ids0[keep], tab[keep,], NULL)
    ref$original <- which(keep)[ref$original]
    expect_identical(out, ref)

    w <- runif(nobs)
    out <- csaw:::.check_test_inputs(ids0, tab, w)
    keep <- !is.na(ids0)
    ref <- csaw:::.check_test_inputs(ids0[keep], tab[keep,], w[keep])
    ref$original <- which(keep)[ref$original]
    expect_identical(out, ref)

    # Behaves on empty inputs.
    out <- csaw:::.check_test_inputs(ids[0], tab[0,], NULL)
    expect_identical(out$ids, integer(0))
    expect_identical(out$groups, character(0))
    expect_identical(out$tab, tab[0,])
    expect_identical(out$weight, numeric(0))
    expect_identical(out$original, integer(0))

    # Checking errors.
    expect_error(csaw:::.check_test_inputs(ids, tab[0,], NULL), "is not TRUE")
    expect_error(csaw:::.check_test_inputs(ids, tab, runif(10)), "is not TRUE")
})

set.seed(320003)
test_that("column parsers for test results are working correctly", {
    tab <- data.frame(logFC=rnorm(1000), PValue=runif(1000))
    expect_identical(csaw:::.parseFCcol(NULL, tab), 1L)
    expect_identical(csaw:::.parseFCcol("logFC", tab), 1L)
    expect_identical(csaw:::.parseFCcol(1, tab), 1L)

    # Handles multiple inputs.
    tab2 <- data.frame(logFC.A=rnorm(1000), logFC.B=runif(1000))
    expect_identical(csaw:::.parseFCcol(NULL, tab2), 1:2)
    expect_identical(csaw:::.parseFCcol(2, tab2), 2L)
    expect_identical(csaw:::.parseFCcol(c("logFC.B", "logFC.A"), tab2), 2:1)

    expect_error(csaw:::.parseFCcol(NULL, tab2, multiple=FALSE), "exactly one column")
    expect_error(csaw:::.parseFCcol("YAY", tab2), "failed to match")

    # Parses p-value columns.
    expect_identical(csaw:::.getPValCol(NULL, tab), 2L)
    expect_identical(csaw:::.getPValCol("PValue", tab), 2L)
    expect_identical(csaw:::.getPValCol(2, tab), 2L)
    expect_error(csaw:::.getPValCol("urgh", tab), "failed to find")
})