[BioC] html report of hyperGTest question

[Seth Falcon]

Hi Siarhei,

Siarhei Manakou <sm7 at sanger.ac.uk> writes:
> However, when i tried to do similar for KEGG pathways and PFAM domains 
> through the following:
[snip]

> -the "problem" with these reports is:
> 1)unlike in GO report there is no "Term" column  which human can 
> understand, and only KEGG/PFAM ids are listed

This should easy to add for KEGG since we have a KEGG annotation
package that maps KEGG ids to names.  I'm not sure yet about PFAM
since I don't know if we have an annotation source within BioC that
maps PFAM ids to more meaningful names.

> 2)to make things worse - there is no html links from these ids, and to 
> see what are the things i have to paste them individually into the 
> google etc.

This is also possible.

> So is there an easy way to add links to the descriptive column to the 
> HTML reports  and to add HTML links to them?

Depends on your definition of easy.  The coding task should not be too
difficult and what is done for GO can be used as a template.

+ seth

-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
BioC: http://bioconductor.org/
Blog: http://userprimary.net/user/