[BioC] Fwd: GO terms: Annotation for HumanMethylation450

[Tim Triche, Jr.]

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