[BioC] Gene Ontology: Shortest path from root to node

[Marc Carlson]

Also I forgot to mention,

You can get the immediate parent to any term by using the appropriate 
PARENTS object.  So for example:

get("GO:0006955", GOBPPARENTS)

Will tell you that there are TWO immediate parents for this term.  Which 
is the situation I was describing earlier.


   Marc


On 01/14/2013 11:09 AM, Marc Carlson wrote:
> Hi Nicos,
>
> You could use the GO.db package to get at this.  In there you will 
> find an object called GOBPANCESTOR which acts like a classic R 
> environment object and can be used with the get() method to pull out 
> the ancestor terms of a given term all the way back to the root.
>
> So for your example you could have done this:
>
> library(GO.db)
> get("GO:0008150", GOBPANCESTOR)
>
> And you can see that the only ancestor to this term is in fact the 
> root node: "all"
>
>
> What about terms further down?  Well the same trick works for all the 
> terms to get their ancestor terms:
> get("GO:0006955", GOBPANCESTOR)
>
>
>
> So you probably want to do something a bit like this:
>
> length(get("GO:0006955", GOBPANCESTOR))
>
> And (for example) compare that to:
>
> length(get("GO:0008150", GOBPANCESTOR))
>
> etc.
>
>
> Of course it's all a little bit more complicated than that because the 
> gene ontologies are actually DAGs (so terms can have more than one 
> route back to the main node), and so your ancestors list may be longer 
> than just the simple path back to the "all" node.  And in fact in the 
> example I gave above this is true for the further down term 
> "GO:0006955", which has two routes back to the main node, and hence 
> it's "distance" (as hinted at by length) has been inflated by one in 
> this case.
>
>
> Anyhow, I hope this helps,
>
>
>   Marc
>
>
>
>
>
> On 01/14/2013 07:47 AM, WoA [guest] wrote:
>> Given some GO BP terms for a gene I wish to find out, which of the 
>> terms has more specific meaning. I wish to find out the length of the 
>> shortest path between the BP Root term(GO:0008150) and the given 
>> term. Is there any suitable way to do that using any R package?
>>
>> Like something equivalent to:
>> my $length = $node->lengthOfShortestPathToRoot;
>>
>> in Perl's "GO-TermFinder" package.
>>
>> Thanks in advance
>>
>>   -- output of sessionInfo():
>>
>>> sessionInfo()
>> R version 2.13.1 (2011-07-08)
>> Platform: i386-pc-mingw32/i386 (32-bit)
>>
>> locale:
>> [1] LC_COLLATE=English_United States.1252
>> [2] LC_CTYPE=English_United States.1252
>> [3] LC_MONETARY=English_United States.1252
>> [4] LC_NUMERIC=C
>> [5] LC_TIME=English_United States.1252
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> -- 
>> Sent via the guest posting facility at bioconductor.org.
>>
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