[BioC] GOstats: another problem

[John Zhang]

>
>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.

Sorry, I forgot to mention that you need to have the developmental version of 
GO, which can be obtained by:

> library(reposTools)
> install.packages2("GO", develOK = TRUE)


>
>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
>>
>>
>
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Jianhua Zhang
Department of Biostatistics
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084