[BioC] GOstats: another problem

[Simon Lin]

John:

One more question to bother you. I have GO_1.5.1 installed.

But GOMFOFFSPRINGS is not part of the environment variable; neither is
GOLOCUSID.

See below:

> get("GO:0003700", OFFSPRING)
Error in get("GO:0003700", OFFSPRING) :
        Object "OFFSPRING" not found

> GO
<environment: 020372E8>

> GOMFOFFSPRINGS
Error: Object "GOMFOFFSPRINGS" not found

> GOMFCHILDREN
<environment: 02E1ADF0>

> GOLOCUSID
Error: Object "GOLOCUSID" not found
>

Any suggestions?

Thanks!

Simon


----- Original Message ----- 
From: "John Zhang" <jzhang at jimmy.harvard.edu>
To: <simon.lin at duke.edu>
Cc: <bioconductor at stat.math.ethz.ch>
Sent: Friday, July 30, 2004 2:57 PM
Subject: Re: [BioC] GOstats:


>
> >How to find all the off-springs (not only direct children) of a GO term,
say
> >"GO:0003700"?
>
> >library(GO)
> >get("GO:0003700", GOMFOFFSPRING)
> [[1]]
> [1] "GO:0003705"
>
>
> >And how to find all the LocusLink IDs associated with these GO terms?
> >Take these two questions together, I want to find all the LL-IDs
associated
> >with a GO node at certain level.
>
> > mget(unlist(get("GO:0003700", GOMFOFFSPRING)), GOLOCUSID)
>  IDA   IDA   IDA   IDA   IEA   NAS   NAS   NAS    NR   TAS   TAS   TAS
TAS
> 17268 18771 20473 81646 25714  1050 31883  9569  7020 17877 17878 17927
17928
>   TAS   TAS   TAS   TAS   TAS   TAS   TAS   TAS   TAS   TAS   TAS   TAS
>  2034  2494  3091  3394  4617   463  4654  4784  5813  5989  5991  7023
>
>
> >
> >I read the vignettes, but am not sure on how to do the above.
> >
> >Thanks!
> >
> >Simon
> >
> >_______________________________________________
> >Bioconductor mailing list
> >Bioconductor at stat.math.ethz.ch
> >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>
> Jianhua Zhang
> Department of Biostatistics
> Dana-Farber Cancer Institute
> 44 Binney Street
> Boston, MA 02115-6084
>
>