GOstats: another problem
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John Zhang ★ 2.9k
@john-zhang-6
Last seen 7.7 years ago
> >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@jimmy.harvard.edu> >To: <simon.lin@duke.edu> >Cc: <bioconductor@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@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 >> >> > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > >_______________________________________________ >Bioconductor mailing list >Bioconductor@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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Simon Lin ▴ 210
@simon-lin-461
Last seen 7.7 years ago
John: It works! Thanks! It is a very clever idea to put the offspring into a hash table. Thus, recursive retrieving is avoided. Best regards, Simon ----- Original Message ----- From: "John Zhang" <jzhang@jimmy.harvard.edu> To: <simon.lin@duke.edu> Cc: <bioconductor@stat.math.ethz.ch> Sent: Monday, August 02, 2004 8:20 AM 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) > > >
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Park, Richard ▴ 220
@park-richard-227
Last seen 7.7 years ago
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@jimmy.harvard.edu] Sent: Monday, August 02, 2004 8:21 AM To: simon.lin@duke.edu Cc: bioconductor@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@jimmy.harvard.edu> >To: <simon.lin@duke.edu> >Cc: <bioconductor@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@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 >> >> > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > >_______________________________________________ >Bioconductor mailing list >Bioconductor@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 _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
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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@jimmy.harvard.edu] > Sent: Monday, August 02, 2004 8:21 AM > To: simon.lin@duke.edu > Cc: bioconductor@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@jimmy.harvard.edu> >> To: <simon.lin@duke.edu> >> Cc: <bioconductor@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@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 >>> >>> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
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John Zhang ★ 2.9k
@john-zhang-6
Last seen 7.7 years ago
>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@jimmy.harvard.edu] >Sent: Monday, August 02, 2004 8:21 AM >To: simon.lin@duke.edu >Cc: bioconductor@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@jimmy.harvard.edu> >>To: <simon.lin@duke.edu> >>Cc: <bioconductor@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@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 >>> >>> >> >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor@stat.math.ethz.ch >>https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >> >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor@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 > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > >_______________________________________________ >Bioconductor mailing list >Bioconductor@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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