[BioC] probesets from a KEGGHyperGParams instance

[James W. MacDonald]

Hi Louisa,

That should be really easy. If you look at the code for 
Category:::htmlReportFromDf, you can see that it just takes the 
data.frame created by the call to summary(hypt, htmlLinks=TRUE) and then 
uses the xtable package to create the html. You could just create the 
data.frame, then get all the probeIDs using the annotation package, and 
then just add the probe IDs to the existing data.frame and output using 
xtable.

You might want to take the probe IDs and wrap them in <P>ProbeID</P> 
first, so they each take up a row, rather than being one long string 
that runs off the page.

HTH,

Jim



Louisa A Rispoli/AS/EXP/UTIA wrote:
> Jim-
> 
> Thank you for the prompt reply. I am using affy ids and performing the
> analysis similar to your description. I was just trying to figure out if
> there was a way to append the htmlReport to include the geneIDsByCategory
> or affy probes without making my head or computer explode. Thank you again
> for the help.
> 
> Louisa
> 
> 
> 
> "If we knew what we were doing, it wouldn't be called Research." - Albert
> Einstein
> 
> Louisa Rispoli, Ph.D. Reproductive Physiology
> Department of Animal Science
> University of Tennessee, Knoxville
> A105 Johnson Animal Research and Teaching Unit
> 1750 Alcoa Highway
> Knoxville, TN 37920
> phone:(865) 946-1874
> fax:(865) 946-1010
> email: lrispoli at utk.edu
> 
> 
> 
> 
>                                                                            
>              "James W.                                                     
>              MacDonald"                                                    
>              <jmacdon at med.umic                                          To 
>              h.edu>                    Louisa A Rispoli/AS/EXP/UTIA        
>                                        <larispoli at mail.ag.utk.edu>         
>              10/30/2008 03:24                                           cc 
>              PM                        bioconductor at stat.math.ethz.ch      
>                                                                    Subject 
>                                        Re: [BioC] probesets from a         
>                                        KEGGHyperGParams instance           
>                                                                            
>                                                                            
>                                                                            
>                                                                            
>                                                                            
>                                                                            
> 
> 
> 
> 
> Hi Louisa,
> 
> With the new SQLite-based annotation packages this should be much more
> simple, although there isn't anything that I know of to give you direct
> results.
> 
> Since you use the term 'probeset' I will take the liberty of assuming
> you are using an Affy chip of some sort. Let's say you have a vector of
> significant probesets that you used to do the hypergeometric analysis.
> You then converted to Entrez Gene IDs and then did the KEGG
> hypergeometric analysis. An example:
> 
> ## fake up some data
>  > library(GOstats)
>  > library(hgu95av2.db)
>  > probeids <- Lkeys(hgu95av2PATH[sample(1:1000, 200)])
>  > egids <- unique(getEG(probeids, "hgu95av2"))
>  > univ <- unique(getEG(Lkeys(hgu95av2PATH), "hgu95av2"))
>  > p <- new("KEGGHyperGParams", geneIds = egids, universeGeneIds = univ,
> annotation = "hgu95av2")
>  > hypt <- hyperGTest(p)
>  > summary(hypt)
>     KEGGID       Pvalue OddsRatio  ExpCount Count Size Term
> 1   05218 1.992936e-07  8.600189 1.8950675    12   58 Melanoma
> [snip..]
> 
> You can also get a nice HTML output using htmlReport():
> 
>  > htmlReport(hypt, file="output.html",summary.args=list(htmlLinks=TRUE))
> 
> So let's say we are completely enthralled with that first term (because
> we are skin cancer researchers and stuff ;-D). Let's see what probeids
> in our significant set map to that term:
> 
>  > prbs <- probeids[probeids %in% get("05218", revmap(hgu95av2PATH))]
>  > prbs
>   [1] "1706_at"   "1654_at"   "1593_at"   "1859_s_at" "1340_s_at"
> "1269_at"
>   [7] "1322_at"   "1504_s_at" "1542_at"   "1526_i_at" "1570_f_at"
> "1713_s_at"
> 
> 
> Best,
> 
> Jim
> 
> Louisa A Rispoli/AS/EXP/UTIA wrote:
>> To anyone with a lot more experience.
>>
>> I have been trying to read through all the helps and vignettes for a
> simple
>> way to get the probesets that went into producing significance of KEGG
> term
>> after running hypergeometric test for KEGG. I have found probeSetSummary
>> for GO terms and hyperGoutput (also for GO terms) but nothing
> corresponding
>> for the KEGG. Was hoping someone had a simple methodology for retrieval.
>>
>> Thanks
>>
>> Louisa
>>
>>
>> "If we knew what we were doing, it wouldn't be called Research." - Albert
>> Einstein
>>
>> Louisa Rispoli, Ph.D. Reproductive Physiology
>> Department of Animal Science
>> University of Tennessee, Knoxville
>> A105 Johnson Animal Research and Teaching Unit
>> 1750 Alcoa Highway
>> Knoxville, TN 37920
>> phone:(865) 946-1874
>> fax:(865) 946-1010
>> email: lrispoli at utk.edu
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> 
> --
> James W. MacDonald, M.S.
> Biostatistician
> Hildebrandt Lab
> 8220D MSRB III
> 1150 W. Medical Center Drive
> Ann Arbor MI 48109-0646
> 734-936-8662
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662