Supports organism detection from Ensembl identifier or genome build.

detectOrganism(object)

Arguments

object

character.

Value

character(1). Full latin organism name. Stops on match failure.

Details

Only the first match is returned. We're using a while loop approach here so we can skip transgenes or spike-ins. The function fails after a maximum of 50 unknowns, for speed.

Note

BiocGenerics::organism() character method conflicts with annotate package, which gets loaded into the namespace when DESeq2 is attached. Instead, we're exporting the character method here as a separate function named detectOrganism.

Supported organisms

  • Caenorhabditis elegans (roundworm)

  • Danio rerio (zebrafish)

  • Drosophila melanogaster (fruitfly)

  • Gallus gallus (chicken)

  • Homo sapiens (human)

  • Mus musculus (mouse)

  • Ovis aries (sheep)

  • Rattus norvegicus (rat)

  • Saccharomyces cerevisiae (yeast)

See also

Examples

## Match by gene identifier. detectOrganism("ENSG00000000003")
#> Error: Failed to detect organism.
## Match by genome build. detectOrganism("GRCh38") # Ensembl
#> Error: Failed to detect organism.
detectOrganism("hg38") # UCSC
#> Error: Failed to detect organism.
## Match by alternate organism name. detectOrganism("H. sapiens")
#> Error: Failed to detect organism.
detectOrganism("hsapiens")
#> Error: Failed to detect organism.
## The function will skip transgenes/spike-ins until we find a match. detectOrganism(c("EGFP", "TDTOMATO", "ENSG00000000003"))
#> Error: Failed to detect organism.
## But it only returns the first match, if there are multiple genomes. detectOrganism(c("ENSG00000000003", "ENSMUSG00000000001"))
#> Error: Failed to detect organism.