tests/testthat/test-src_organism-select.R

In Organism.dplyr: dplyr-based Access to Bioconductor Annotation Resources

context("src_organism-select")

suppressPackageStartupMessages({
    library(TxDb.Hsapiens.UCSC.hg38.knownGene)
})
txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene

hg38light <- hg38light()
src <- src_organism(dbpath=hg38light)

test_that("keytypes", {
    expect_equal(class(keytypes(src)), "character")
    expect_true(length(keytypes(src)) > 0)
})

test_that("columns", {
    expect_equal(class(columns(src)), "character")
    expect_true(length(columns(src)) > 0)
})

test_that("keys", {
    expect_error(keys(src, "foo"))
    expect_equal(class(keys(src)), "character")
    expect_true(length(keys(src)) > 0)
    expect_true(all(keys(src, "tx_id") %in% keys(txdb, "TXID")))
})

test_that("select", {
    columns_src <- c("entrez", "tx_id", "tx_name","exon_id")
    keytype_src <- "tx_name"
    columns_txdb <- c("GENEID", "TXID", "TXNAME","EXONID")
    keytype_txdb <- "TXNAME"

    keys <- head(keys(src, keytype_src))
    rs_src <- select(src, keys, columns_src, keytype_src) %>% collect()
    rs_txdb <- select(txdb, keys, columns_txdb, keytype_txdb)

    expect_equal(dim(rs_src), dim(rs_txdb))
    expect_equal(
        rs_src[order(rs_src[,keytype_src]),]$tx_id,
        rs_txdb[order(rs_txdb[,keytype_txdb]),]$TXID
    )
})

test_that("mapIds", {
    keys <- head(keys(src, "tx_name"))

    rs_src <- mapIds(src, keys, "exon_id", "tx_name")
    rs_txdb <- mapIds(txdb, keys, "EXONID", "TXNAME")

    expect_equal(rs_src, rs_txdb)
})