[BioC] GOstats: another problem

[John Zhang]

>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?

If you would like to save the output as it is for later use, please have a look 
at the save function. Otherwise, you need to tell us a little more about what 
you are trying to do.


>
>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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>>Bioconductor mailing list
>>Bioconductor at stat.math.ethz.ch
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>>
>>_______________________________________________
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>>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
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
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Jianhua Zhang
Department of Biostatistics
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084