organism_species: Organism and species accessors

In Bioconductor/BiocGenerics: S4 generic functions used in Bioconductor

Organism and species accessors

Description

Get or set the organism and/or species of an object.

Usage

organism(object)
organism(object) <- value

species(object)
species(object) <- value

Arguments

object	An object to get or set the organism or species of.
value	The organism or species to set on object.

Value

organism should return the scientific name (i.e. genus and species, or genus and species and subspecies) of the organism. Preferably in the format "Genus species" (e.g. "Homo sapiens") or "Genus species subspecies" (e.g. "Homo sapiens neanderthalensis").

species should of course return the species of the organism. Unfortunately there is a long history of misuse of this accessor in Bioconductor so its usage is now discouraged (starting with BioC 3.1).

Note

TO DEVELOPERS:

species has been historically misused in many places in Bioconductor and is redundant with organism. So implementing the species accessor is now discouraged (starting with BioC 3.1). The organism accessor (returning the scientific name) should be implemented instead.

See Also

• http://bioconductor.org/packages/release/BiocViews.html#___Organism for browsing the annotation packages currently available in Bioconductor by organism.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• organism,character-method and organism,chromLocation-method in the annotate package for examples of specific organism methods (defined for character and chromLocation objects).

• species,AnnotationDb-method in the AnnotationDbi package for an example of a specific species method (defined for AnnotationDb objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

## organism() getter:
organism
showMethods("organism")

library(annotate)
showMethods("organism")
selectMethod("organism", "character")
selectMethod("organism", "chromLocation")

## organism() setter:
`organism<-`
showMethods("organism<-")

## species() getter:
species
showMethods("species")

library(AnnotationDbi)
selectMethod("species", "AnnotationDb")

## species() setter:
`species<-`
showMethods("species<-")

Bioconductor/BiocGenerics documentation built on Nov. 5, 2023, 6:10 a.m.