[BioC] simLL method in GOstats

[Maria Persico]

Dear bioconductor mailing list,

I have some pairs of genes and I would like to measure their "distances"
on the GO molecular function graph.

So I wrote this lines of code:

distances<-numeric(100)
for (i in 1:100){
 goanal<-simLL(as.character(hmapr$V1[i]),as.character(hmapr$V2[i]),"MF")
 print(goanal$sim)
 distances[i]<-goanal$sim
 rm(goanal)
 }

where hmapr$V1 and hmapr$V2 are the vectors in which I have the locus link
identifiers of my genes.

When I run the script, in a few time I obtain
"Error: invalid subscript type".

I noticed that there are problems with the pair of llID where the script
stops.

 Is there a way to bypass the problem, to jump to the next pair
of genes after putting NaN in the distances vector?

Thanks a lot,

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