detectOrganism: Detect organism

View source: R/detectOrganism.R

detectOrganismR Documentation

Detect organism

Description

Supports organism detection from Ensembl identifier or genome build.

Usage

detectOrganism(object)

Arguments

object

character.

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.

Value

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

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)

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.

See Also

BiocGenerics::organism().

Examples

## Match by gene identifier.
detectOrganism("ENSG00000000003")

## Match by genome build.
detectOrganism("GRCh38") # Ensembl
detectOrganism("hg38") # UCSC

## Match by alternate organism name.
detectOrganism("H. sapiens")
detectOrganism("hsapiens")

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

## But it only returns the first match, if there are multiple genomes.
detectOrganism(c("ENSG00000000003", "ENSMUSG00000000001"))

acidgenomics/r-acidgenomes documentation built on Jan. 12, 2024, 4:06 a.m.