[BioC] Fwd: GO terms: Annotation for HumanMethylation450
Jinyan Huang
jhuang at hsph.harvard.edu
Wed Apr 3 20:07:49 CEST 2013
Marc,
When I update my R to 2.15.2, I still have the error.
R
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> 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 at 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 at 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 at gmail.com> wrote:
>>>> Buy more RAM :-)
>>>>
>>>> --t
>>>>
>>>> On Apr 3, 2013, at 6:59 AM, Jinyan Huang <jhuang at 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 at Term,y at GOID,y at 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 at 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 at 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 at 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 at 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 at 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 at 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
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