Get or set the organism and/or species of an object.
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An object to get or set the organism or species of.
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.
"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).
species has been historically misused in many places in Bioconductor
and is redundant with
organism. So implementing the
accessor is now discouraged (starting with BioC 3.1). The
accessor (returning the scientific name) should be implemented
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,chromLocation-method in the
annotate package for examples of specific
methods (defined for character and chromLocation
species,AnnotationDb-method in the
AnnotationDbi package for an example of a specific
species method (defined for AnnotationDb
BiocGenerics for a summary of all the generics defined in the BiocGenerics package.
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## 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<-")
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