[BioC] GOstats: another problem

[Sean Davis]

Richard,

In what format would you like the output?  What are you going to use if 
for?  If you just want one long vector, you can do:

unlist(get("GO:0003824",GOMFOFFSPRING))

Sean

On Aug 2, 2004, at 11:49 AM, Park, Richard wrote:

> Is there any easy way to output the results of get("GO:0003824", 
> GOMFOFFSPRING) for example.
> I have tried using the standard output functions write, and 
> write.table, is there any easy way to output really long lists?
>
> thank,
> Richard
>
>
> -----Original Message-----
> From: John Zhang [mailto:jzhang at jimmy.harvard.edu]
> Sent: Monday, August 02, 2004 8:21 AM
> To: simon.lin at duke.edu
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] GOstats: another problem
>
>
>
>>
>> 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
>
> _______________________________________________
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