On 09/14/2017 02:23 PM, Laurent Gatto wrote:
On 14 September 2017 15:15, Hervé Pagès wrote:
Hi,
Note that right now the name of the Ontology getter matches the
name of the corresponding field in all our annotations:
> library(org.Hs.eg.db)
> org.Hs.egGO[["92610"]][["GO:0005622"]]
On 14 September 2017 15:15, Hervé Pagès wrote:
> Hi,
>
> Note that right now the name of the Ontology getter matches the
> name of the corresponding field in all our annotations:
>
>> library(org.Hs.eg.db)
>
>> org.Hs.egGO[["92610"]][["GO:0005622"]]
>$GOID
>[1] "GO:0005622"
>
>
Hi,
Note that right now the name of the Ontology getter matches the
name of the corresponding field in all our annotations:
> library(org.Hs.eg.db)
> org.Hs.egGO[["92610"]][["GO:0005622"]]
$GOID
[1] "GO:0005622"
$Evidence
[1] "IEA"
$Ontology
[1] "CC"
> library(GO.db)
> G
On 09/12/2017 01:58 PM, Vincent Carey wrote:
For this particular problem, it may be worth noting that
https://urldefense.proofpoint.com/v2/url?u=http-3A__geneontology.org_page_ontology-2Dstructure&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ECJZN8XlNzgWTqEBb
For this particular problem, it may be worth noting that
http://geneontology.org/page/ontology-structure
describes CC, MF, BP as "sub-ontologies" of GO. AnnotationDbi might replace
its Ontology() with subontology() to acquire those tokens.
On Tue, Sep 12, 2017 at 4:28 PM, Michael Lawrence wrot
I think I'm going to vote for the policy that methods with identical
signatures are currently unsupported by the methods package. It's
tough to imagine how they might work in any reliable and natural way,
and they totally break the methods package currently.
In the grand scheme of things, generics
Hi Herve,
I understand that there is a clash between the two identical methods.
Both packages seem to have good reasons to implement their own
`Ontology,character`. Such clashes are relatively frequent.
My issue really is that when unloading AnnotationDbi's namespace,
`Ontology,character` is rem
Hi Laurent,
The 2 Ontology,character methods defined in AnnotationDbi and
rols do very different things. The 1st one expects a vector of
GO IDs and returns the GO sub-ontologies that they belong to:
> Ontology(c("GO:009", "GO:012", "GO:006"))
GO:009 GO:012 GO:006
"M
Dear all,
This is a follow up to a previous email regarding the Ontology generic
function, that is now in the BiocGenerics package. It seems that my
problem was not only that both rols and AnnotationDbi defined the same
generic, but they also both defined Ontology,character.
> library("rols")
T
