organism_species: Organism and species accessors

Description Usage Arguments Value Note See Also Examples

Description

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

Usage

1
2
3
4
5
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

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
## 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<-")

BiocGenerics documentation built on April 17, 2021, 6:01 p.m.