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

[Maria Persico]

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