[BioC] Getting GO terms and other annotation for Golub data set

[Sean Davis]

Mick,

GOHyperG is a useful function for that.  Also, the vignettes are 
available at http://www.bioconductor.org.  Finally, to get a list of 
all the functions in a package, do:

help(package=GOstats)

for example.

Sean

On Feb 7, 2005, at 8:20 AM, michael watson ((IAH-C)) wrote:

> Thanks Sean.
>
> I don't know whether my installation of GOstats has gone awry at some
> point, but there doesn't seem to be a manual or vignette for the 
> package
> in C:\Program Files\R\rw2001\library\GOstats\doc.  There is an
> index.html but it is next to empty.
>
> So if I have two affy ids, I can get the GO terms easily, but it's not
> immediately obvious which functions in GOstats I could use to to see if
> those two affy ids are related in a functional sense.
>
> -----Original Message-----
> From: Sean Davis [mailto:sdavis2 at mail.nih.gov]
> Sent: 07 February 2005 13:05
> To: michael watson (IAH-C)
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] Getting GO terms and other annotation for Golub 
> data
> set
>
>
>
> On Feb 7, 2005, at 5:21 AM, michael watson ((IAH-C)) wrote:
>>
>> So now I have the GO and KEGG metaData packages, and I know how to
>> query
>> them at a very low level.  My next step will be to write some code to
>> take a group of affy identifiers, query these packages and see if they
>> all seem to hit the same KEGG pathway, or have GO terms in common.
> Has
>> anyone done this before and put it in a nice package, or do I write it
>> from scratch?
>>
>
> The GOstats package does this for GO.  You could use that directly for
> the GO stuff.  For the KEGG stuff, I think you would have to write
> something, but it shouldn't be too hard.  Also, there are now several
> websites that allow you to do this (not an R solution, but perhaps a
> good first-pass).
>
> Sean