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