Hi Jinyan, The code I showed you before will get you all the GO TERMS and their DESCRIPTIONS into a single data frame (without using too much RAM): library(GO.db) k = keys(GOTERM) ## k is now all the GOIDs that we actually have Terms for. ## If you use another source of GOIDs, you might want to call unique() on that 1st. ## In order to save time. ## Then just call select like I showed you before result = select(GO.db, keys =k, cols=c("DEFINITION","TERM")) ## Then you can use merge() to attach that onto your gene IDs later on. I hope this helps, Marc On 04/03/2013 08:28 AM, Tim Triche, Jr. wrote: > 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)da ta.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,s ep="\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_MolCe ll_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 >> >> >> -- >> Best wishes, >> >> Jinyan HUANG

May need to do require(AnnotationDbi) require(Homo.sapiens) ## or GO.db, or whatever in order for that to work. On Wed, Apr 3, 2013 at 11:07 AM, Jinyan Huang <jhuang@hsph.harvard.edu>wrote: > Marc, > > When I update my R to 2.15.2, I still have the error. > > R > > R version 2.15.2 (2012-10-26) -- "Trick or Treat" > Copyright (C) 2012 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > Platform: x86_64-unknown-linux-gnu (64-bit) > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > > > ids = c( "GO:0008150", "GO:0001869") > > result = select(GO.db, keys =ids, cols=c("DEFINITION","TERM")) > Error: could not find function "select" > > sessionInfo() > R version 2.15.2 (2012-10-26) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > On Wed, Apr 3, 2013 at 1:40 PM, Marc Carlson <mcarlson@fhcrc.org> wrote: > > Hi Jinyan, > > > > The code I showed you before will get you all the GO TERMS and their > > DESCRIPTIONS into a single data frame (without using too much RAM): > > > > library(GO.db) > > k = keys(GOTERM) ## k is now all the GOIDs that we actually have Terms > > for. > > ## If you use another source of GOIDs, you might want to call unique() > > on that 1st. > > ## In order to save time. > > ## Then just call select like I showed you before > > result = select(GO.db, keys =k, cols=c("DEFINITION","TERM")) > > > > ## Then you can use merge() to attach that onto your gene IDs later on. > > > > I hope this helps, > > > > > > Marc > > > > > > > > On 04/03/2013 08:28 AM, Tim Triche, Jr. wrote: > >> Probably so. I will look into it. Thanks for the report > >> > >> --t > >> > >> On Apr 3, 2013, at 8:21 AM, Jinyan Huang <jhuang@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@gmail.com> > wrote: > >>>> Buy more RAM :-) > >>>> > >>>> --t > >>>> > >>>> On Apr 3, 2013, at 6:59 AM, Jinyan Huang <jhuang@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@Term > ,y@GOID,y@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@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@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/Illum inaHumanMethylation450k.db.html > >>>>>>>> > >>>>>>>> On Fri, Mar 29, 2013 at 12:29 PM, Tim Triche, Jr. < > tim.triche@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@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@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@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 > >>> > >>> > >>> -- > >>> Best wishes, > >>> > >>> Jinyan HUANG > > > > > > -- > Best wishes, > > Jinyan HUANG > -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]

> library(GO.db) Loading required package: AnnotationDbi Loading required package: BiocGenerics Attaching package: ?BiocGenerics? The following object(s) are masked from ?package:stats?: xtabs The following object(s) are masked from ?package:base?: anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply, setdiff, table, tapply, union, unique Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: DBI >ids = c( "GO:0008150", "GO:0001869") > result = select(GO.db, keys =ids, cols=c("DEFINITION","TERM")) Error in eval(expr, envir, enclos) : object 'GODEFINITION' not found > sessionInfo() R version 2.15.2 (2012-10-26) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] GO.db_2.7.1 RSQLite_0.11.2 DBI_0.2-5 [4] AnnotationDbi_1.18.4 Biobase_2.16.0 BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] IRanges_1.14.4 stats4_2.15.2 On Wed, Apr 3, 2013 at 2:07 PM, Jinyan Huang <jhuang at="" hsph.harvard.edu=""> wrote: > Marc, > > When I update my R to 2.15.2, I still have the error. > > R > > R version 2.15.2 (2012-10-26) -- "Trick or Treat" > Copyright (C) 2012 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > Platform: x86_64-unknown-linux-gnu (64-bit) > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > >> ids = c( "GO:0008150", "GO:0001869") >> result = select(GO.db, keys =ids, cols=c("DEFINITION","TERM")) > Error: could not find function "select" >> sessionInfo() > R version 2.15.2 (2012-10-26) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > On Wed, Apr 3, 2013 at 1:40 PM, Marc Carlson <mcarlson at="" fhcrc.org=""> wrote: >> Hi Jinyan, >> >> The code I showed you before will get you all the GO TERMS and their >> DESCRIPTIONS into a single data frame (without using too much RAM): >> >> library(GO.db) >> k = keys(GOTERM) ## k is now all the GOIDs that we actually have Terms >> for. >> ## If you use another source of GOIDs, you might want to call unique() >> on that 1st. >> ## In order to save time. >> ## Then just call select like I showed you before >> result = select(GO.db, keys =k, cols=c("DEFINITION","TERM")) >> >> ## Then you can use merge() to attach that onto your gene IDs later on. >> >> I hope this helps, >> >> >> Marc >> >> >> >> On 04/03/2013 08:28 AM, Tim Triche, Jr. wrote: >>> 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/ht ml/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_Mol Cell_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 >>>> >>>> >>>> -- >>>> Best wishes, >>>> >>>> Jinyan HUANG >> > > > > -- > Best wishes, > > Jinyan HUANG -- Best wishes, Jinyan HUANG

Hi Jinyan, 1st of all, please do the following to update some of your very old packages: source("http://bioconductor.org/biocLite.R") biocLite(c("AnnotationDbi","GO.db") ## Then you can load the libraries like this: library(GO.db) ## and use the cols method to see what you can ask for like this: cols(GO.db) For more explanations, please look at this vignette here: http://www.bioconductor.org/packages/2.11/bioc/vignettes/AnnotationDbi /inst/doc/IntroToAnnotationPackages.pdf Thanks, Marc On 04/03/2013 11:36 AM, Jinyan Huang wrote: > Thank you. It works now. > > result = select(GO.db, keys =k, cols=c("DEFINITION","TERM")) > > Here what kind of columns can I select? e.g if I do not want GO term's > Evidence is IEA. > > In the help page, I cannot find such information. > > On Wed, Apr 3, 2013 at 2:11 PM, Tim Triche, Jr. <tim.triche at="" gmail.com=""> wrote: >> May need to do >> >> require(AnnotationDbi) >> require(Homo.sapiens) ## or GO.db, or whatever >> >> in order for that to work. >> >> >> >> On Wed, Apr 3, 2013 at 11:07 AM, Jinyan Huang <jhuang at="" hsph.harvard.edu=""> >> wrote: >>> Marc, >>> >>> When I update my R to 2.15.2, I still have the error. >>> >>> R >>> >>> R version 2.15.2 (2012-10-26) -- "Trick or Treat" >>> Copyright (C) 2012 The R Foundation for Statistical Computing >>> ISBN 3-900051-07-0 >>> Platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> R is free software and comes with ABSOLUTELY NO WARRANTY. >>> You are welcome to redistribute it under certain conditions. >>> Type 'license()' or 'licence()' for distribution details. >>> >>> Natural language support but running in an English locale >>> >>> R is a collaborative project with many contributors. >>> Type 'contributors()' for more information and >>> 'citation()' on how to cite R or R packages in publications. >>> >>> Type 'demo()' for some demos, 'help()' for on-line help, or >>> 'help.start()' for an HTML browser interface to help. >>> Type 'q()' to quit R. >>> >>>> ids = c( "GO:0008150", "GO:0001869") >>>> result = select(GO.db, keys =ids, cols=c("DEFINITION","TERM")) >>> Error: could not find function "select" >>>> sessionInfo() >>> R version 2.15.2 (2012-10-26) >>> Platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> locale: >>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >>> [7] LC_PAPER=C LC_NAME=C >>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> On Wed, Apr 3, 2013 at 1:40 PM, Marc Carlson <mcarlson at="" fhcrc.org=""> wrote: >>>> Hi Jinyan, >>>> >>>> The code I showed you before will get you all the GO TERMS and their >>>> DESCRIPTIONS into a single data frame (without using too much RAM): >>>> >>>> library(GO.db) >>>> k = keys(GOTERM) ## k is now all the GOIDs that we actually have Terms >>>> for. >>>> ## If you use another source of GOIDs, you might want to call unique() >>>> on that 1st. >>>> ## In order to save time. >>>> ## Then just call select like I showed you before >>>> result = select(GO.db, keys =k, cols=c("DEFINITION","TERM")) >>>> >>>> ## Then you can use merge() to attach that onto your gene IDs later on. >>>> >>>> I hope this helps, >>>> >>>> >>>> Marc >>>> >>>> >>>> >>>> On 04/03/2013 08:28 AM, Tim Triche, Jr. wrote: >>>>> 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_M olCell_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 >>>>>> >>>>>> -- >>>>>> Best wishes, >>>>>> >>>>>> Jinyan HUANG >>> >>> >>> -- >>> Best wishes, >>> >>> Jinyan HUANG >> >> >> >> -- >> A model is a lie that helps you see the truth. >> >> Howard Skipper > >