[BioC] Fwd: GO terms: Annotation for HumanMethylation450

[Tim Triche, Jr.]

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.
>>>>>>>> 
>>>>>>>> _______________________________________________
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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