May need to do

require(AnnotationDbi)
require(Homo.sapiens) ## or GO.db, or whatever

in order for that to work.



On Wed, Apr 3, 2013 at 11:07 AM, Jinyan Huang <jhuang@hsph.harvard.edu>wrote:

> Marc,
>
> When I update my R to 2.15.2, I still have the error.
>
> R
>
> R version 2.15.2 (2012-10-26) -- "Trick or Treat"
> Copyright (C) 2012 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
>   Natural language support but running in an English locale
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
> > ids = c( "GO:0008150", "GO:0001869")
> > result = select(GO.db, keys =ids, cols=c("DEFINITION","TERM"))
> Error: could not find function "select"
> > sessionInfo()
> R version 2.15.2 (2012-10-26)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=C                 LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> On Wed, Apr 3, 2013 at 1:40 PM, Marc Carlson <mcarlson@fhcrc.org> wrote:
> > Hi Jinyan,
> >
> > The code I showed you before will get you all the GO TERMS and their
> > DESCRIPTIONS into a single data frame (without using too much RAM):
> >
> > library(GO.db)
> > k = keys(GOTERM)  ## k is now all the GOIDs that we actually have Terms
> > for.
> > ## If you use another source of GOIDs, you might want to call unique()
> > on that 1st.
> > ## In order to save time.
> > ## Then just call select like I showed you before
> > result = select(GO.db, keys =k, cols=c("DEFINITION","TERM"))
> >
> > ## Then you can use merge() to attach that onto your gene IDs later on.
> >
> > I hope this helps,
> >
> >
> >    Marc
> >
> >
> >
> > On 04/03/2013 08:28 AM, Tim Triche, Jr. wrote:
> >> Probably so. I will look into it. Thanks for the report
> >>
> >> --t
> >>
> >> On Apr 3, 2013, at 8:21 AM, Jinyan Huang <jhuang@hsph.harvard.edu>
> wrote:
> >>
> >>> Are there any others efficient way to do this? I just thought there
> >>> are some problem in my code.
> >>>
> >>> On Wed, Apr 3, 2013 at 11:14 AM, Tim Triche, Jr. <tim.triche@gmail.com>
> wrote:
> >>>> Buy more RAM :-)
> >>>>
> >>>> --t
> >>>>
> >>>> On Apr 3, 2013, at 6:59 AM, Jinyan Huang <jhuang@hsph.harvard.edu>
> wrote:
> >>>>
> >>>>> When I want to get all GO terms on IlluminaHumanMethylation450k.
> There
> >>>>> is a memory problem. It uses more than 10G memory.
> >>>>>
> >>>>> GOids <- lapply(res2, function(x) unlist(lapply(x, function(y)
> y$GOID)))
> >>>>> GOterms <- lapply(GOids, function(x) mget(x, GOTERM, ifnotfound=NA))
> >>>>> Error: memory exhausted (limit reached?)
> >>>>> Execution halted
> >>>>>
> >>>>>
> >>>>>
> --------------------------------------Get_all_GO.R----------------------------------------------
> >>>>>
> >>>>> library(IlluminaHumanMethylation450k.db)
> >>>>> ## allow both singly- and multiply-mapped probes (e.g. for SYMBOL)
> >>>>> IlluminaHumanMethylation450kGOall
> >>>>> <-toggleProbes(IlluminaHumanMethylation450kGO,'all')
> >>>>> ## now let's look at the differences that result from toggleProbes()
> >>>>> mapped_probes_toggled <-
> mappedkeys(IlluminaHumanMethylation450kGOall)
> >>>>> res <- mget(mapped_probes_toggled, IlluminaHumanMethylation450kGOall,
> >>>>> ifnotfound=NA)
> >>>>> res2 <- lapply(res, function(x) x[sapply(x, function(y)
> y['Evidence']!='IEA')])
> >>>>> ## fetch the GOIDs from the unencumbered toggled map, to get terms
> for them
> >>>>> library(GO.db)
> >>>>> GOids <- lapply(res2, function(x) unlist(lapply(x, function(y)
> y$GOID)))
> >>>>> GOterms <- lapply(GOids, function(x) mget(x, GOTERM, ifnotfound=NA))
> >>>>>
> d<-lapply(GOterms,function(x)do.call(rbind,lapply(x,function(y)data.frame(y@Term
> ,y@GOID,y@Ontology))))
> >>>>> df<-do.call(rbind,d)
> >>>>> len <- sapply(d,function(x)length(x[,1]))
> >>>>> probes <- rep(names(d),len)
> >>>>> df.out<-data.frame(probes=probes,df)
> >>>>> names(df.out)<-c("probe","GoTerm","GOID","GOCategory")
> >>>>>
> write.table(df.out,"GO_all.txt",quote=F,row.names=F,col.names=T,sep="\t")
> >>>>>
> >>>>>
> ----------------------------------------------------------------------------------------------------------------
> >>>>>
> >>>>> On Tue, Apr 2, 2013 at 7:29 PM, Tim Triche, Jr. <
> tim.triche@gmail.com> wrote:
> >>>>>> Hi all,
> >>>>>>
> >>>>>> Not sure how I managed not to cc: the list on this initially.
> Here's some GO.db code with a sort of "moral" to it ;-)
> >>>>>>
> >>>>>> --t
> >>>>>>
> >>>>>> Begin forwarded message:
> >>>>>>
> >>>>>> library(IlluminaHumanMethylation450k.db)
> >>>>>>
> >>>>>> ## allow both singly- and multiply-mapped probes (e.g. for SYMBOL)
> IlluminaHumanMethylation450kGOall
> <-toggleProbes(IlluminaHumanMethylation450kGO, 'all')
> >>>>>>
> >>>>>> ## now let's look at the differences that result from toggleProbes()
> >>>>>> mapped_probes_default <- mappedkeys(IlluminaHumanMethylation450kGO)
> >>>>>> mapped_probes_toggled <-
> mappedkeys(IlluminaHumanMethylation450kGOall)
> >>>>>> multimapped <- setdiff( mapped_probes_toggled,
> mapped_probes_default )
> >>>>>>
> >>>>>> res0 <- mget(head(multimapped), IlluminaHumanMethylation450kGO,
> ifnotfound=NA)
> >>>>>> res <- mget(head(multimapped), IlluminaHumanMethylation450kGOall,
> ifnotfound=NA)
> >>>>>>
> >>>>>> ## fetch the GOIDs from the unencumbered toggled map, to get terms
> for them
> >>>>>>
> >>>>>> library(GO.db)
> >>>>>> GOids <- lapply(res, function(x) unlist(lapply(x, function(y)
> y$GOID)))
> >>>>>> GOterms <- lapply(GOids, function(x) mget(x, GOTERM, ifnotfound=NA))
> >>>>>> head(GOterms)
> >>>>>>
> >>>>>>
> >>>>>>> I'll add this to the docs (next release)
> >>>>>>>
> >>>>>>> thanks,
> >>>>>>>
> >>>>>>> --t
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> On Fri, Mar 29, 2013 at 11:24 AM, Fabrice Tourre <
> fabrice.ciup@gmail.com> wrote:
> >>>>>>>> Tim,
> >>>>>>>>
> >>>>>>>> Thank you very much for your reply.
> >>>>>>>> I have a list of probe list.
> >>>>>>>> Do you a example script for me to get the GO terms, instead of GO
> ID?
> >>>>>>>>
> >>>>>>>> The Documentation is not very clear for this.
> >>>>>>>>
> http://www.bioconductor.org/packages/2.11/data/annotation/html/IlluminaHumanMethylation450k.db.html
> >>>>>>>>
> >>>>>>>> On Fri, Mar 29, 2013 at 12:29 PM, Tim Triche, Jr. <
> tim.triche@gmail.com> wrote:
> >>>>>>>>> Oddly enough, the paper from UCSD with Illumina's folks on it
> (*) used the
> >>>>>>>>> IlluminaHumanMethylation450k.db package (which I am currently
> rebuilding to
> >>>>>>>>> have a startup message about toggleProbes()) to annotate both
> CpG islands
> >>>>>>>>> and GO terms.
> >>>>>>>>>
> >>>>>>>>> (*)
> >>>>>>>>>
> http://idekerlab.ucsd.edu/publications/Documents/Hannum_MolCell_2012.pdf
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> On Fri, Mar 29, 2013 at 8:49 AM, Fabrice Tourre <
> fabrice.ciup@gmail.com>
> >>>>>>>>> wrote:
> >>>>>>>>>> Dear list,
> >>>>>>>>>>
> >>>>>>>>>> In the annotation file of Infinium HumanMethylation450 BeadChip,
> >>>>>>>>>>
> >>>>>>>>>>
> http://support.illumina.com/documents/MyIllumina/b78d361a-def5-4adb-ab38-e8990625f053/HumanMethylation450_15017482_v.1.2.csv
> >>>>>>>>>>
> >>>>>>>>>> for each probe set, they do not have annotation for GO terms,
> pathways.
> >>>>>>>>>>
> >>>>>>>>>> As they have done in the annotation file:
> HG-U133_Plus_2.na32.annot.csv.
> >>>>>>>>>>
> >>>>>>>>>> Is there some bioconductor package to annotated the Infinium
> >>>>>>>>>> HumanMethylation450 probes? Given a probe, feed back the GO
> terms and
> >>>>>>>>>> pathways.
> >>>>>>>>>>
> >>>>>>>>>> Thank you very much in advance.
> >>>>>>>>>>
> >>>>>>>>>> _______________________________________________
> >>>>>>>>>> Bioconductor mailing list
> >>>>>>>>>> Bioconductor@r-project.org
> >>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >>>>>>>>>> Search the archives:
> >>>>>>>>>>
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> --
> >>>>>>>>> A model is a lie that helps you see the truth.
> >>>>>>>>>
> >>>>>>>>> Howard Skipper
> >>>>>>>
> >>>>>>>
> >>>>>>> --
> >>>>>>> A model is a lie that helps you see the truth.
> >>>>>>>
> >>>>>>> Howard Skipper
> >>>>>>        [[alternative HTML version deleted]]
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> Bioconductor mailing list
> >>>>>> Bioconductor@r-project.org
> >>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >>>>>> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>>>>
> >>>>>
> >>>>> --
> >>>>> Best wishes,
> >>>>>
> >>>>> Jinyan HUANG
> >>>
> >>>
> >>> --
> >>> Best wishes,
> >>>
> >>> Jinyan HUANG
> >
>
>
>
> --
> Best wishes,
>
> Jinyan HUANG
>



-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

	[[alternative HTML version deleted]]

