[BioC] association of clinical phenotype to sequence data

[Wolfgang Huber]

Dear Ian,

I guess pretty much all of the regression and classification methods 
provided in R packages on CRAN and Bioconductor could be of potential use.

Depending on your data, it would seem appropriate not to treat each 
sequence position and variant as independent, but to consider their 
phylogenetic tree.

This paper and others by these authors might be relevant:
http://nar.oxfordjournals.org/cgi/content/full/31/13/3850
Geno2pheno: estimating phenotypic drug resistance from HIV-1 genotypes
N. Beerenwinkel et al.

  Best wishes
	Wolfgang


> Hi all,
> 
> I have a dataset consisting of sequence data from specific viral genes
> that I'm trying to correlate to data from indicators of disease outcome
> (CD4+ count, viral load etc). Are there any packages currently available
> through bioconductor that would be suitable for exploring associations
> within the data?
> 
> Many Thanks
> 
> Ian Cheeseman 
> 
> Research Degree Student
> Room 360
> London School of Hygiene & Tropical Medicine
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-- 

Best wishes
   Wolfgang

------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber