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)
})
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