Organism and species accessors
Get or set the organism and/or species of an object.
organism(object) organism(object) <- value species(object) species(object) <- value
object |
An object to get or set the organism or species of. |
value |
The organism or species to set on |
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).
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.
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.
## 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<-")Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.