[BioC] R script

[fhong@salk.edu]

> Hi Fangxin
> can you send me the R script you mentioned in your
> e-mail below:
> "Thanks, Robert.
> I made the functions myself using the handout from the
> short Course(this June), it turns out to be pretty
> simple. So I would provide the R script of doing this
> if somebody ask for.
> Good day.
> Fangxin"


You  guys are fast! I attached the R script below. I used ATH1 array as
example, you can change it to whatever system you are using.
For example, I am looking for genes (on ATH1 array) that contain
"replication" in GOterm.


Good luck!
Fangxin


#######
#function used to search for GO terms
###########
GOTerm2Tag=function(term)
{
  GTL=eapply(GOTERM,function(x) {
     grep(term,x at Term,value=TRUE)
  })
  Glen=sapply(GTL,length)
  names(GTL[Glen>0])
}

##Example  (get GOID of the terms that contain replication)
GO.rep=GOTerm2Tag("replication")

########
#GO for all genes on ATH1 array
########
GO.Ath1=mget(AffyID,ath1121501GO)  ##GO for all genes on ATH1
GOID.Ath1=sapply(GO.Ath1, function(x) {
    ##GO term for all genes on ATH1
    onts=sapply(x, function(z) z$GOID)
    })


#########
#FUNCTION: Search for genes that contain the target GOID
#########
GOID2Gene=function(GOID,GOID.Ath1)
{
   ##GOID: target GOID you are looking in gene
   GOID.finder=sapply(GOID.Ath1,function(x) {
     grep(GOID,unlist(x),value=TRUE)
  })
  GOID.finder.len=sapply(GOID.finder,length)
  names(GOID.finder.len>0)
}


##Example: output AffyID of genes that has GOID "GO:0016563"
> GOID2Gene("GO:0016563",GOID.Ath1)


######Example####################################
#look for all genes that involve in replication
#output AffyID of all genes involving in replication
##########
AffyID.rep=c()
for ( i in GO.rep)
{
  AffyID.rep=c(AffyID.rep,GOID2Gene(i,GOID.Ath1))
}
AffyID.rep.unique=unique(AffyID.rep)




--------------------
Fangxin Hong  Ph.D.
Plant Biology Laboratory
The Salk Institute
10010 N. Torrey Pines Rd.
La Jolla, CA 92037
E-mail: fhong at salk.edu
(Phone): 858-453-4100 ext 1105