context("Ensembl annotations")
mat <- .ucscMatrix
keep <- as.logical(mat[, "ensembldb"])
mat <- mat[keep, , drop = FALSE]
## Note that we're running at transcript level here to check the gene merge.
##
## Potential issues:
## - *Caenorhabditis elegans*
## - Invalid transcript IDs.
## - *Canis familiaris*
## - Using the full *Canis lupus familiaris* won't match.
## - *Saccharomyces cerevisiae*
## - Invalid gene IDs.
## - Iinvalid transcript IDs.
## - No gene names.
with_parameters_test_that(
"UCSC genome build remaps", {
object <- makeGRangesFromEnsembl(
organism = organism,
genomeBuild = genomeBuild,
level = "transcripts"
)
expect_s4_class(object, "GRanges")
},
organism = mat[, "organism"],
genomeBuild = mat[, "ucsc"]
)
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