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 <mtmorgan@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 <ruipbarradas@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

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