Hi,
The organism and species accessors (getters and setters) are now generic
functions in BiocGenerics (>= 0.13.8).
To my knowledge all the packages in devel (except rsbml) that define
(or use) these accessors were modified to use these new generics.
Please let me know if I forgot some.
Some clarifications (just added now in BiocGenerics 0.13.9) in the
man page for these generics:
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 DEVELOPPERS:
‘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.
Cheers,
H.
On 03/10/2015 07:28 AM, Laurent Gatto wrote:
Dear all,
Two possible candidates for BiocGenerics:
GenomeInfoDb::species
standardGeneric for "species" defined from package "GenomeInfoDb"
function (x)
standardGeneric("species")
<environment: 0x7278130>
Methods may be defined for arguments: x
Use showMethods("species") for currently available ones.
AnnotationDbi::species
standardGeneric for "species" defined from package "AnnotationDbi"
function (x)
standardGeneric("species")
<environment: 0x89feb18>
Methods may be defined for arguments: x
Use showMethods("species") for currently available ones.
and
annotate::organism
standardGeneric for "organism" defined from package "annotate"
function (object)
standardGeneric("organism")
<environment: 0x8771908>
Methods may be defined for arguments: object
Use showMethods("organism") for currently available ones.
GenomeInfoDb::organism
standardGeneric for "organism" defined from package "GenomeInfoDb"
function (x)
standardGeneric("organism")
<environment: 0x8232da0>
Methods may be defined for arguments: x
Use showMethods("organism") for currently available ones.
Best wishes,
Laurent
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Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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