[BioC] simLL method in GOstats to measure distances between yeast genes

[Robert Gentleman]

Hi Maria,
   The simLL function relies on have Entrez gene (used to be LocusLink 
IDs). Which seem to be the type of identifiers you are providing - so 
you have no need of ygs98 - that I can see.
   Now the first one of your identifiers: "855134" if you check does not 
have any GO annotation - so you won't get a GO graph for it.

   And the human one works because both genes are annotated for the GO 
category you are interested in. The result does not mean that the 
function reads any other library - it does just what it says it does. 
Locus/Entrez to GO - but if there is no GO anntation then you will get NA.

  Best wishes,
    Robert

Maria Persico wrote:
> Dear All,
>  I did some modifications in function simLL to allow this function access
> to ygs98 annotation:
> 
> this is the code:
> 
> simLL2<-function (ll1, ll2, Ontology = "MF", measure = "LP", dropCodes =
> NULL)
> {
>     require(ygs98)
> #or library(ygs98)
>     wh = match.arg(Ontology, c("MF", "BP", "CC"))
>     ll1GO = .getWHEC(ll1, wh, dropCodes)
>     ll2GO = .getWHEC(ll2, wh, dropCodes)
>     dataenv = get(paste("GO", wh, "PARENTS", sep = ""), mode =
> "environment")
>     g1 = GOGraph(ll1GO, dataenv)
>     g2 = GOGraph(ll2GO, dataenv)
> .....
> ....etc etc
> 
> Then, I run the function with these 2 yeast geneID:
> 
> aa = simLL2("855134", "851236", "BP")
> 
> and I obtain
> 
>>aa
> 
> [1] NA
> 
> If I run the function with 2 human llID(aa = simLL2("9184", "3547",
> "BP")), the function give me the right result.This means that the function
> reads the hgu95av2 library.
> 
> How can I adapt the simmLL function to work with yeast annotation?
> 
> Thanks,
> 
> Maria
> 
> 
> 
> 
> Maria Persico
> MINT database, Cesareni Group
> Universita' di Tor Vergata, via della Ricerca Scientifica
> 00133 Roma, Italy
> Tel: +39 0672594315
> FAX: +39 0672594766
> e-mail: maria at cbm.bio.uniroma2.it
> 
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