[BioC] Please Help with Starr Package

[Martin Morgan]

Noah Dowell wrote:
> Hello To All,
> 
> The early processing and normalization functions within Starr all seem to be working quite nicely so I quite grateful  for this package, but I have stumbled in the graphing of the Affymetrix tiling array data.  
> 
> The vignette for the package has a nice example of plotting data in relation to all gene TSS's which I am trying to replicate.  To do this I need a GFF file that has genomic features such as "gene" or "TSS" , etc. (I am also interested in other features such as telomeres, centromeres so the transcriptAnno.gff in the example will be quite limited in utility.)
> 
> 
> 
> How do I create such a file? What files do I need?  Where can I obtain them? (goldenpath, SGD, etc.??)

Hi Noah --

One might get this info from a variety of sources, biomaRt::getBM being
one rich possibility. Aim to create the gff with rtracklayer::export.

  library(biomaRt)
  listMart()
  listDatasets(useMart("fungal_mart_3"))
  mart = useMart("fungal_mart_3", "scerevisiae_eg_gene")
  listAttributes(mart)

being a start.


Martin

> 
> 
> 
> 
> I found the writeGFF function that uses a CEL and bpmap file to make a GFF but as far as I can tell that does not have genomic feature annotation information.
> 
> Thank you in advance for any help!!
> 
> noah
> 
> 
> 
>> sessionInfo()
> R version 2.10.0 (2009-10-26) 
> i386-apple-darwin9.8.0 
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods   base     
> 
> other attached packages:
> [1] Starr_1.2.0        affxparser_1.18.0  affy_1.24.0        Ringo_1.10.0       Matrix_0.999375-31 lattice_0.17-26   
> [7] limma_3.2.1        RColorBrewer_1.0-2 Biobase_2.6.0     
> 
> loaded via a namespace (and not attached):
>  [1] affyio_1.14.0        annotate_1.24.0      AnnotationDbi_1.8.0  DBI_0.2-4            genefilter_1.28.0   
>  [6] MASS_7.3-3           preprocessCore_1.8.0 pspline_1.0-13       RSQLite_0.7-3        splines_2.10.0      
> [11] survival_2.35-7      xtable_1.5-5      
> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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