[BioC] Fwd: GO terms: Annotation for HumanMethylation450

[Jinyan Huang]

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