tests/testthat/test_mapping.R

In steveped/chipExtra: Additional functions for working with ChIP-Seq data

# We need a combination of ranges which do & don't map
genes <- GRanges(c("chr1:2-10:*", "chr1:25-30:-", "chr1:31-40:+"))
genes$gene_id <- paste0("gene", seq_along(genes))
## Add a promoter for each gene
prom <- promoters(genes, upstream = 1, downstream = 1)
## Add an enhancer in gene2 & to the right of gene3
enh <- GRanges(c("chr1:20", "chr1:50"))
enh$which <- c("gene2", "gene1 (gi)")
## Map the last enhancer to gene1's promoter
gi <- InteractionSet::GInteractions(prom[1], enh[2])
mcols(gi) <- c()
## Now define key ranges
gr <- GRanges(paste0("chr1:", seq(0, 50, by = 10)))
gr$via_ol <- CharacterList(
    list(NULL, "gene1", NULL, c("gene2", "gene3"), "gene3", NULL)
)
gr$via_prom <- CharacterList(
    list("gene1", NULL, NULL, c("gene2", "gene3"), NULL, NULL)
)
gr$via_enh_gap5 <- CharacterList(
    list(NULL, NULL, "gene2", NULL, NULL, NULL)
)
gr$via_gi <- CharacterList(
    list("gene1", NULL, NULL, NULL, NULL, "gene1")
)

test_that(".mapFeatures produces expected output from promoters", {
    mapped_prom <- .mapFeatures(gr, prom, genes, "gene_id", 0, 0)
    expect_true(is(mapped_prom, "data.frame"))
    expect_equal(
        table(mapped_prom$range),
        structure(
            1:2, .Dim = 2L,
            .Dimnames = structure(list(c("chr1:0", "chr1:30")), .Names = ""),
            class = "table"
        )
    )
    expect_equal(mapped_prom$gene_id, c("gene1", "gene2", "gene3"))
})

test_that(".mapFeatures produces expected output from enhancers", {
    expect_equal(.mapFeatures(gr, enh, genes, "gene_id", 0, 5)$gene_id, "gene2")
})

test_that(".mapFeatures returns NULL & errors where expected", {
    expect_null(.mapFeatures(gr, enh, genes, "gene_id", 0, 0))
    expect_null(.mapFeatures(GRanges()))
    expect_null(.mapFeatures(NULL))
    expect_null(.mapFeatures(gr, GRanges("chr1:100"), .gr2feat = 0))
    expect_null(.mapFeatures(gr))
    expect_error(.mapFeatures(gr, prom, genes, "", 0, 0))
})

test_that(".mapGi produces the expected output",{
    mapped_gi <- .mapGi(gr, gi, genes, "gene_id", 0, 0)
    expect_true(is(mapped_gi, "data.frame"))
    expect_equal(
        table(mapped_gi$range),
        structure(
            c(`chr1:0` = 1L, `chr1:50` = 1L), .Dim = 2L,
            .Dimnames = structure(list(c("chr1:0", "chr1:50")), .Names = ""),
            class = "table"
        )
    )
    expect_equal(mapped_gi$gene_id, c("gene1", "gene1"))
})

test_that("mapGi returns NULL & errors where expected", {
    expect_error(.mapGi(gr, gi, genes, "", 0, 0))
    expect_null(.mapGi(gr[NULL], gi, genes, "gene_id", 0, 0))
    expect_null(.mapGi(gr, gi[NULL], genes, "gene_id", 0, 0))
    expect_null(.mapGi(gr, NULL, genes, "gene_id", 0, 0))
})

test_that(".mapWithin produces the expected output", {
    gr <- GRanges(c("chr1:5", "chr1:21-30", "chr1:30"))
    genes <- GRanges(c("chr1:15-25", "chr1:29"))
    genes$gene_id <- paste0("gene", 1:2)
    mapped_within <- .mapWithin(gr, genes, "gene_id", 5)
    expect_true(is(mapped_within, "data.frame"))
    expect_equal(
        mapped_within$range,
        as.character(gr)[c(2, 2, 3)]
    )
    expect_equal(mapped_within$gene_id, paste0("gene", c(1, 2, 2)))
})

test_that(".mapWithin returns NULL & errors when expected", {
    expect_null(.mapWithin(NULL))
    expect_null(.mapWithin(gr))
    expect_error(.mapWithin(gr, genes, ""))
})

test_that("mapByFeature errors correctly", {
    expect_error(mapByFeature(NULL))
    expect_error(suppressMessages(mapByFeature(gr, genes, cols = "")))
})

test_that("mappingArg Checks behave correctly", {
    expect_error(.checkMappingArgs(), "query ranges must be provided")
    expect_error(
        .checkMappingArgs(NULL), "query object must be a GenomicRanges object"
    )
    expect_error(
        .checkMappingArgs(GRanges(), .cols = NULL),
        "At least one gene/ID column must be specified"
    )
    expect_message(
        .checkMappingArgs(gr, genes, prom, enh, gi, "", 0),
        "No requested columns were able to be found"
    )
    expect_message(
        .checkMappingArgs(gr, genes, prom, enh, gi, "gene_id", ""),
        "All distance arguments must be numeric"
    )
    expect_message(
        .checkMappingArgs(gr, "", prom, enh, gi, "gene_id", 0),
        "Genes must be provided as"
    )
    expect_message(
        .checkMappingArgs(gr, genes, "", enh, gi, "gene_id", 0),
        "Promoters must be"
    )
    expect_message(
        .checkMappingArgs(gr, genes, prom, "", gi, "gene_id", 0),
        "Enhancers must be"
    )
    expect_message(
        .checkMappingArgs(gr, genes, prom, enh, "", "gene_id", 0),
        "Interactions must be"
    )
})