[Bioc-devel] Genomics analysis results class

[Vincent Carey]

The things that I remember doing that capture analysis results are
some classes in MLInterfaces for dealing with classification and
clustering, and in GGtools for managing eQTL search results.   One
package that seems relevant to Luigi's concern is GeneAnswers, which
is at 0.99, from the Northwestern U group.

Some other things to think about -- you seem to be collecting
quantitative information on genomic elements.  Will it be relevant to
be able to display these in a genome browser?  If so, designing
software that transforms this information into classes used for
browsing with rtracklayer seems to make sense.  annaffy is a nice and
fairly general approach to throwing textual information and links
relevant to genes into HTML for interactive browsing.

Finally, class design/reuse decisions are probably best conducted by
spelling out the methods that need to be present.  Clearly a gene set
structure is relevant, and sets and translations among nomenclatures
are well-handled by GSEABase classes.  If you feel you will often need
to filter results to those relevant to a pathway, a subsetting
mechanism will be important to have.

On Wed, Oct 7, 2009 at 3:06 PM, Luigi Marchionni <marchion at jhu.edu> wrote:
> Dear developers,
> my name is Luigi Marchionni, I am Instructor in Oncology at Johns Hopkins.
> I have ongoing research on various biological problems and I make use of
> GSEA like methods for which I wrote my own package.
> I'd like to upload that in Bioconductor and for this reason I am updating my
> code to reuse as much as possible already implemented S4 classes.
>
> For the gene sets I am using GSEABase classes, however I did not find an
> existing class for results from genomics analyses.
> I thought in the first place to extend the MultiSet class from Biobase, but
> this does not seem to be completely appropriate (I have results from
> different platforms and technologies, i.e. microarray and SAGE).
>
> Right now I use a list of data.frames, each one storing the features
> identifiers and the ranking statistics from the genomics analyses
> (additional information could be obviously added in additional slots). See
> the object ex.Stats below as an example:
>
>> class(ex.Stats)
> [1] "list"
>> str(ex.Stats)
> List of 2
>  $ ex.hgu133a :'data.frame':    100 obs. of  6 variables:
>  ..$ ID       : chr [1:100] "200763_s_at" "200062_s_at" "208834_x_at"
> "214631_at" ...
>  ..$ logFC    : num [1:100] -8.09 -6.71 -5.92 5.97 5.82 ...
>  ..$ t        : num [1:100] -43.8 -31 -30.5 28.8 27.3 ...
>  ..$ P.Value  : num [1:100] 1.89e-96 2.85e-73 3.25e-72 1.49e-68 3.18e-65 ...
>  ..$ adj.P.Val: num [1:100] 1.27e-92 9.57e-70 7.26e-69 2.50e-65 4.26e-62 ...
>  ..$ B        : num [1:100] 204 154 152 144 136 ...
>  $ ex.hgu95av2:'data.frame':    100 obs. of  6 variables:
>  ..$ ID       : chr [1:100] "31957_r_at" "35777_at" "32412_at" "32539_at"
> ...
>  ..$ logFC    : num [1:100] -7.76 -6.93 -5.66 5.72 5.68 ...
>  ..$ t        : num [1:100] -41 -31.3 -28.5 27 26 ...
>  ..$ P.Value  : num [1:100] 7.05e-92 8.77e-74 8.49e-68 2.16e-64 3.29e-62 ...
>  ..$ adj.P.Val: num [1:100] 4.73e-88 2.94e-70 1.90e-64 3.63e-61 4.41e-59 ...
>  ..$ B        : num [1:100] 194 155 142 134 130 ...
>
> This works just fine, however, I do not want to reinvent the wheel...
> I was discussing with Rafa and he suggested that before I go any further
> with coding I inquire with you guys if anything like this already exists.
> He said that Vincent Carey might have already something for that.
> Is that true? Do you have any suggestion?
>
> I thank all of you in advance,
>
> Luigi Marchionni
>
> --
> Ulisse: "Considerate la vostra semenza:
> fatti non foste a viver come bruti,
> ma per seguir virtute e canoscenza".
> (Dante, Divina Commedia, Canto XXVI)
> --
>     G-C
>    T---A    Luigi Marchionni, M.D., Ph.D.
>   C----G    The Sidney Kimmel Comprehensive Cancer Center
> G-------C    Johns Hopkins University -  School of Medicine
>  A------T     1550 Orleans St., CRB2, Rm 554
>    C----G    Baltimore, MD, 21231, USA
>    G--C    Tel: (001) 410-502-8179
>     C-G    Fax: (001) 410-502-5742
>    T---A    e-mail: marchion at jhmi.edu
>   G-----C    URL: http://astor.som.jhmi.edu/~marchion/
>  A-------T
>
> _______________________________________________
> Bioc-devel at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>