[BioC] Fwd: GO terms: Annotation for HumanMethylation450

[Jinyan Huang]

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.
>>>>>>>
>>>>>>> _______________________________________________
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>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> 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]]
>>>
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>>
>>
>>
>> --
>> Best wishes,
>>
>> Jinyan HUANG



-- 
Best wishes,

Jinyan HUANG