Hi I think I asked the wrong question. Apologies. Actually I want all the GO BP annotations for my organism and from them I want to retain only those annotations which annotate less than a specified number of genes. (say <1000 genes)
I hope I have put it clearly. sorry again. Thanks! On Sun, Jul 7, 2013 at 6:55 AM, Martin Morgan <mtmor...@fhcrc.org> wrote: > In Bioconductor, install the annotation package > > > http://bioconductor.org/packages/release/BiocViews.html#___AnnotationData > > corresponding to your chip, e.g., > > source("http://bioconductor.org/biocLite.R";) > biocLite("hgu95av2.db") > > then load it and select the GO terms corresponding to your probes > > library(hgu95av2.db) > lkup <- select(hgu95av2.db, rownames(dat), "GO") > > then use standard R commands to find the probesets that have the GO id > you're interested in > > keep = lkup$GO %in% "GO:0006355" > unique(lkup$PROBEID[keep]) > > Ask follow-up questions about Bioconductor packages on the Bioconductor > mailing list > > http://bioconductor.org/help/mailing-list/mailform/ > > Martin > ----- Rui Barradas <ruipbarra...@sapo.pt> wrote: > > Hello, > > > > Your question is not very clear, maybe if you post a data example. > > To do so, use ?dput. If your data frame is named 'dat', use the > following. > > > > dput(head(dat, 50)) # paste the output of this in a post > > > > > > If you want to get the rownames matching a certain pattern, maybe > > something like the following. > > > > > > idx <- grep("GO:0006355", rownames(dat)) > > dat[idx, ] > > > > > > Hope this helps, > > > > Rui Barradas > > > > > > Em 07-07-2013 07:01, Chirag Gupta escreveu: > > > Hello everyone > > > > > > I have a dataframe with rows as probeset ID and columns as samples > > > I want to check the rownames and find which are those probes are > > > transcription factors. (GO:0006355 ) > > > > > > Any suggestions? > > > > > > Thanks! > > > > > > > ______________________________________________ > > R-help@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > > and provide commented, minimal, self-contained, reproducible code. > -- *Chirag Gupta* Department of Crop, Soil, and Environmental Sciences, 115 Plant Sciences Building, Fayetteville, Arkansas 72701 [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
