Description Usage Arguments Value Note See Also Examples
Get or set the organism and/or species of an object.
1 2 3 4 5 |
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.
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<-")
|
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