tests/testthat/test-annotation.R

In recount: Explore and download data from the recount project

context("Annotation")

library("GenomicRanges")

ranges_both <- reproduce_ranges("both", db = "Gencode.v25")
exons <- ranges_both$exon
genes <- ranges_both$gene
exons_ensembl <- reproduce_ranges("exon", db = "EnsDb.Hsapiens.v79")

test_that("Annotation length", {
    expect_equal(length(exons), length(genes))
    expect_gte(length(genes), length(recount_genes))
    expect_gte(length(exons), length(recount_exons))
    expect_gte(length(exons_ensembl), 65774)
    expect_equal("ENSG00000000003" %in% names(exons_ensembl), TRUE)
    expect_equal(length(genome(recount_exons)), 25)
    expect_equal("GRCh38" %in% genome(exons_ensembl), TRUE)
    expect_equal(colnames(mcols(recount_genes)), c("gene_id", "bp_length", "symbol"))
    expect_equal(colnames(mcols(genes)), c("gene_id", "bp_length", "symbol"))
})