tests/testthat/test-3modifications.R

In EpiTxDb: Storing and accessing epitranscriptomic information using the AnnotationDbi interface

context("modifications")
test_that("modifications:",{
    etdb_file <- system.file("extdata", "EpiTxDb.Hs.hg38.snoRNAdb.sqlite",
                             package="EpiTxDb")
    etdb <- loadDb(etdb_file)
    actual <- modifications(etdb)
    expect_s4_class(actual,"GRanges")
    expect_equal(colnames(mcols(actual)),c("mod_id","mod_type","mod_name"))
    expect_error(modifications(etdb, columns = c("MOD")),
                 "MOD: no such column in db schema")
    actual <- modifications(etdb, columns = c("MODID","MODTYPE","MODNAME"))
    expect_s4_class(actual,"GRanges")
    expect_equal(colnames(mcols(actual)),c("MODID","MODTYPE","MODNAME"))
    #
    expect_error(modifications(etdb, filter = 1),
                 "NA: no such column in db schema")
    actual <- modifications(etdb, filter = c(mod_id = 1))
    expect_s4_class(actual,"GRanges")
    expect_equal(length(actual),1L)
    # actual <- modifications(etdb, filter = c(mod_id = 236))
    # expect_equal(length(actual),0L)
    #
    actual <- modificationsBy(etdb)
    expect_s4_class(actual,"GRangesList")
    expect_named(actual)
    expect_equal(colnames(mcols(unlist(actual))),
                 c("mod_id","mod","mod_name"))
    actual <- modificationsBy(etdb, by = "specifier")
    expect_s4_class(actual,"GRangesList")
    expect_named(actual)
    actual <- modificationsBy(etdb, by = "reaction")
    expect_s4_class(actual,"GRangesList")
    expect_named(actual)
    actual <- modificationsBy(etdb, by = "modtype")
    expect_s4_class(actual,"GRangesList")
    expect_named(actual)
    expect_named(actual,c("Am","Cm","Gm","Um","Y"))
    actual <- modificationsBy(etdb, by = "specifiertype")
    expect_s4_class(actual,"GRangesList")
    expect_named(actual)
    dbDisconnect(etdb$conn)
})