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/Il luminaHumanMethylation450k.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