[Bioc-sig-seq] BioC2010 Simple RNA-seq Use Case lab

[Steve Lianoglou]

Hi,

On Tue, Oct 5, 2010 at 2:30 PM, pterry at huskers.unl.edu
<pterry at huskers.unl.edu> wrote:
>  Dear bioc-sig-sequencing,
>
> I would like to work thru the BioC2010 workshop lab, http://www.bioconductor.org/help/course-materials/2010/BioC2010/Exercises-SimpleRNAseqUseCase.pdf.
>
> At least three functions and a data set were in a package distributed at the lab in the package HTSandGeneCentricLabs.
>
> geneBounds
> rpkm
> countExonIdsByTxOverlaps
> multiplex_export.txt.gz
>
> Might these functions be incorporated into regular bioconductor packages by now?  Or can you recommend how I might work thru this lab now?

Lots of these can be done with a bit of proficiency with the
GenomicFeatures package.

For instance, there was a thread from a bit over a week ago that
helped the OP get a bit on the way to an RPKM calculation:

http://thread.gmane.org/gmane.science.biology.informatics.conductor/31032

I'm not sure what geneBounds is, but I guess you are looking for the
txstart/end of genes. You can get there by, for example, loading some
test data:

R> library(GenomicFeatures)
R> txdb_file <- system.file("extdata", "UCSC_knownGene_sample.sqlite",
                           package="GenomicFeatures")
R> txdb <- loadFeatures(txdb_file)
R> xcripts <- transcriptsBy(txdb, "gene")
R> gene.bounds <- lapply(xcripts, range)

The rest of your requests should work themselves out within a day or
two of getting to know the rest of the GenomicFeatures functionality.

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact