inst/unitTests/test_mapIdsToRanges.R

In Bioconductor/GenomicFeatures: Query the gene models of a given organism/assembly

txdb <- local({
    fl <- system.file(package = "GenomicFeatures", "extdata",
                      "sample_ranges.rds")
    makeTxDbFromGRanges(readRDS(fl))
})

test_mapIdsToRanges_improper_inputs <- function()
{
    checkException(mapIdsToRanges(txdb, keys = ""),
        "must be a named list")

    checkException(mapIdsToRanges(txdb, keys = "ENST000000271582"),
        "must be a named list")

    checkException(mapIdsToRanges(txdb, keys = list("ENST000000271582")),
        "must be a named list")

    checkException(mapIdsToRanges(txdb,
                                  keys = list(tx_name = "ENST000000271582"),
                                  column = 1),
        "'columns' must be 'NULL' or a character vector")
}

test_mapIdsToRanges_same_order <- function()
{
    keys <- list(tx_name = c("ENST00000371582", "ENST00000371588",
        "ENST00000494752", "ENST00000614008", "ENST00000496771"))
    res <- mapIdsToRanges(txdb, keys = keys, type = "tx")
    checkEquals(names(res), keys[[1]])

    # shuffle the order and make sure it remains equivalent
    for (i in seq_len(10)) {
        keys$tx_name <- sample(keys$tx_name)
        res <- mapIdsToRanges(txdb, keys = keys, type = "tx")
        checkEquals(names(res), keys[[1]])
    }
}

test_mapIdsToRanges_missing_results <- function()
{
    keys <- list(tx_name = c("ENST00000371582", "NOT_FOUND", "ENST00000494752"))
    res <- mapIdsToRanges(txdb, keys = keys, type = "tx")
    checkEquals(names(res), keys$tx_name)

    # shuffle the order and make sure it remains equivalent
    for (i in seq_len(10)) {
        keys$tx_name <- sample(keys$tx_name)
        res <- mapIdsToRanges(txdb, keys = keys, type = "tx")
        checkEquals(names(res), keys$tx_name)
    }
}

test_mapIdsToRanges_duplicate_ranges <- function()
{
    # both of these transcripts are from the same gene
    keys <- list(tx_name = c("ENST00000371582", "ENST00000494752"))
    res <- mapIdsToRanges(txdb, keys = keys, type = "gene")

    #names match input
    checkEquals(names(res), keys[[1]])
    # but values are the same
    checkTrue(all.equal(res[[1]], res[[2]], check.attributes = FALSE))
}

test_mapIdsToRanges_duplicate_ids <- function() {
    keys <- list(tx_name = c("ENST00000371582", "ENST00000494752",
                             "ENST00000371582"))
    res <- mapIdsToRanges(txdb, keys = keys, type = "gene")
    checkEquals(names(res), keys[[1]])
    checkEquals(res[[1]], res[[3]])
}

test_mapRangesToIds_empty <- function()
{
    checkException(mapRangesToIds(txdb, NULL), list())

    checkException(mapRangesToIds(txdb, list()), list())
}

test_mapRangesToIds_matches <- function()
{
    keys <- list(tx_name = c("ENST00000371582", "ENST00000371588",
        "ENST00000494752", "ENST00000614008", "ENST00000496771"))
    res <- mapIdsToRanges(txdb, keys = keys, type = "gene")

    res2 <- mapRangesToIds(txdb, res, "tx")
    checkTrue(keys$tx_name[1] %in% res2[[1]]$tx_name)

    checkTrue(keys$tx_name[2] %in% res2[[2]]$tx_name)
}