Skip to contents

Detect organism

Source: R/detectOrganism.R
detectOrganism.Rd

Supports organism detection from Ensembl identifier or genome build.

Usage

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.

Updated 2023-09-14.

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

BiocGenerics::organism().

Examples

## Match by gene identifier.
detectOrganism("ENSG00000000003")
#> [1] "Homo sapiens"

## Match by genome build.
detectOrganism("GRCh38") # Ensembl
#> [1] "Homo sapiens"
detectOrganism("hg38") # UCSC
#> [1] "Homo sapiens"

## Match by alternate organism name.
detectOrganism("H. sapiens")
#> [1] "Homo sapiens"
detectOrganism("hsapiens")
#> [1] "Homo sapiens"

## The function will skip transgenes/spike-ins until we find a match.
detectOrganism(c("EGFP", "TDTOMATO", "ENSG00000000003"))
#> [1] "Homo sapiens"

## But it only returns the first match, if there are multiple genomes.
detectOrganism(c("ENSG00000000003", "ENSMUSG00000000001"))
#> [1] "Homo sapiens"