/usr/lib/R/site-library/GenomicFeatures/unitTests/test_mapIdsToRanges.R is in r-bioc-genomicfeatures 1.30.0+dfsg-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 | 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)
}
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